The DOI matches its Crossref record; 67 of the 72 references it cites were found in a registry or an index, and 5 are not checked yet; 19 of the 109 sources its claims cite were checked for support.
Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals
Open accessAbstract
The relationships at the root of the animal tree have proven difficult to resolve, with the current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum Ctenophora) are the sister group of all other animals [1-5]. The choice of evolutionary models seems to be at the core of the problem because Porifera tends to emerge as the sister group of all other animals ("Porifera-sister") when site-specific amino acid differences are modeled (e.g., [6, 7]), whereas Ctenophora emerges as the sister group of all other animals ("Ctenophora-sister") when they are ignored (e.g., [8-11]). 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 and that no routinely used evolutionary model can adequately describe both forms of heterogeneity. We show that data-recoding methods [13-15] reduce compositional heterogeneity in these datasets and that models accommodating site-specific amino acid preferences can better describe the recoded datasets. Increased model adequacy is associated with significant topological changes in support of Porifera-sister. Because adequate modeling of the evolutionary process that generated the data is fundamental to recovering an accurate phylogeny [16-20], our results strongly support sponges as the sister group of all other animals and provide further evidence that Ctenophora-sister represents a tree reconstruction artifact. VIDEO ABSTRACT.
Verified 2026-10-06 · 5 references not checked yet
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Written from the paper’s full text.
TL;DR
Feuda et al. use posterior predictive tests to show that two phylogenomic datasets previously supporting Ctenophora-sister are poorly described by standard models, especially for site-specific and lineage-specific compositional heterogeneity. When data are recoded and analyzed with CAT-GTR+G, model adequacy improves and Porifera-sister is favored, leading the authors to conclude that Ctenophora-sister is a tree reconstruction artifact.
Key findings
- All considered models were rejected for site-specific and lineage-specific compositional heterogeneity, but CAT-GTR+G performed best. For WhelanD20-Opistho, PPA-DIV Z scores were 127.35 (WAG), 116.17 (LG), 92.62 (GTR), 104.71 (PF-scheme), and 6.21 (CAT-GTR); for Chang, CAT-GTR gave 6.17. Recoding reduced these values, e.g., Dayhoff-6 + CAT-GTR gave 0.94 for WhelanD20-Opistho and KGB-6 + CAT-GTR gave 0.71 for Chang. For PPA-MAX, all models were strongly rejected, with the smallest absolute Z score being 12.15 (CAT-GTR on Chang).
- WAG+G, LG+G, GTR+G (with or without recoding), and PF-schemes invariably supported Ctenophora-sister (posterior probabilities [PPs] ≥ 1). CAT-GTR+G on amino acid datasets varied by outgroup: WhelanD20-Opistho supported Ctenophora-sister (PP ≥ 1), whereas WhelanD20-Holo and WhelanD20-Choano supported Porifera-sister (PP = 0.68 and 0.77, respectively); Chang under CAT-GTR+G supported Ctenophora-sister (PP ≥ 1).
- CAT-GTR+G analyses of recoded datasets increased support for Porifera-sister. Dayhoff-6 PPs for Porifera-sister were 0.89 (WhelanD20-Opistho), 0.99 (WhelanD20-Holo), 0.95 (WhelanD20-Choano), and 0.74 (Chang); S&R-6 PPs were 0.98, 0.99, 0.94, and 0.62; KGB-6 PPs were 0.42, 0.68, 0.37, and 0.78. Ctenophora-sister received lower support in these analyses.
- Additional tests rejected the claim that Porifera-sister signal is limited to outlier genes: a Shen et al. outlier-excluded dataset still supported Porifera-sister under CAT-GTR+G (PP = 0.98 and 0.99 with and without Dayhoff-6 recoding), and a Dayhoff-6 recoded version of the Whelan et al. 2017 dataset supported Porifera-sister with PP = 1.
Methods
- Posterior predictive analyses (PPAs) tested model adequacy on WhelanD20 (70 taxa) and Chang (77 taxa, 51,940 amino acid positions) using WAG+G, LG+G, GTR+G, optimal PartitionFinder schemes, and CAT-GTR+G. Site-specific amino acid preferences were assessed with PPA-DIV, PPA-CONV, and PPA-VAR; lineage-specific compositional heterogeneity was assessed with PPA-MAX and PPA-MEAN, with results quantified as Z scores.
- Data recoding used Dayhoff-6, S&R-6, and KGB-6. Phylogenetic analyses were performed in PhyloBayes MPI v1.7a for GTR+G and CAT-GTR+G (with and without recoding), and RAxML v8.2.9 was used for the Chang PF-scheme analysis; convergence was assessed with bpcomp and tracecomp.
- Additional analyses applied CAT-GTR+G to a Shen et al. outlier-excluded dataset with and without Dayhoff-6 recoding, and to a Dayhoff-6 recoded version of the Whelan et al. 2017 dataset.
Limitations
- Stated: none of the considered models explicitly accounts for lineage-specific compositional heterogeneity, and all models—including CAT-GTR+G—were strongly rejected in PPA-MAX and PPA-MEAN tests (smallest absolute Z = 12.15). Models that jointly account for site and lineage heterogeneity are noted as computationally too demanding for phylogenomic datasets.
- Stated: recoding can cause signal erosion, although the authors argue this would collapse nodes rather than change the supported topology; also, the CAT-GTR+G analysis of the amino acid version of Chang did not converge well, while all other analyses did.
- Evident: the study’s conclusions depend on a selected set of models and PPA statistics; CAT+G was not directly tested (CAT-GTR+G was used as a representative), and the PartitionFinder protocol excluded some available models such as LG4X.
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Claims the paper makes
40 Not checked yet · 25 Own result · 12 Own interpretation · 3 Partly supported · 3 Own method · 1 Supported so far · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the 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]).”
What the sources say
- Supportedcites [6] Pisani, 2015, Genomic data do not support comb jellies as the sister group to all other animals, Proc. Natl. Acad. Sci. USA source
The Results (pp. 2, 4) report that analyses of the same genomic datasets changed support for Ctenophora-sister and Porifera-sister when outgroup sampling, substitution models, or sequence filtering changed. The paper treats the Ctenophora-sister support as an artifact, but that does not conflict with the claim that both outcomes can be recovered under different analyses. (LLM, conf=0.90)
- Partly supportedcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA sourceExperimental — accuracy not yet measured
The section “Ctenophores Sister to Other Extant Animals and Monophyletic Sponges” reports one analysis in which maximum likelihood supported Ctenophora-sister while Bayesian inference recovered Porifera-sister, though support for the latter was low. The paper does not establish that both hypotheses are generally recovered from the same dataset: in “Placement of Ctenophores Sister to all Remaining Animals Is Not Sensitive to Systematic Errors,” it says its analyses using different models and taxon- and gene-filtering strategies consistently supported Ctenophora-sister. Page numbers are unavailable in our copy. (LLM, conf=0.83)
- Partly supportedcites [42] Pick, 2010, Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships, Mol. Biol. Evol. sourceExperimental — accuracy not yet measured
The paper’s Abstract reports that Dunn et al. recovered Ctenophora-sister, whereas its reanalysis recovered Porifera-sister using the same gene set with expanded taxon sampling. The reanalysis also refined the alignment and expanded the matrix, so it does not establish that both results came from an unchanged dataset. (LLM, conf=0.85)
- Not checked yetcites [45] Dunn, 2008, Broad phylogenomic sampling improves resolution of the animal tree of life, Nature source
- Supportedcites [7] Simion, 2017, A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals, Curr. Biol. source
In “Drastic Effects of Taxon Sampling and Site-Homogeneous versus Site-Heterogeneous Model Type on the Placement of Long Branches” (page unavailable), the paper reports that analyses of its multigene dataset recovered Ctenophora-sister under the LG model but Porifera-sister under the CAT model. It also compares results under different sponge-taxon samplings, supporting the claim that methodological choices can yield both hypotheses from the same dataset. (LLM, conf=0.90)
- Partly supportedcites [43] Philippe, 2011, Resolving difficult phylogenetic questions: why more sequences are not enough, PLoS Biol. sourceExperimental — accuracy not yet measured
In “Issues at the Level of Sequence Alignments,” the paper describes a ctenophore placement in Dunn et al.’s analysis and a Porifera-sister placement after its alignments were corrected and expanded. But it does not establish that both hypotheses are generally supported by the same dataset under different substitution models or gene-sampling strategies; the paper also reports weak support for the revised deep relationships. No page numbers are available in our copy. (LLM, conf=0.84)
- Not checked yetcites [47] Cannon, 2016, Xenacoelomorpha is the sister group to Nephrozoa, Nature 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.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“As phylogenetic methods are less likely to recover artifactual topologies when the models of evolution moreadequatelydescribethedata[16-20],weconcludethatPorifera-sister better represents the phylogenetic signal in the data.”
What the sources say
- Not checked yetcites [16] Goldman, 1993, Statistical tests of models of DNA substitution, J. Mol. Evol. source
- Supportedcites [17] Bollback, 2002, Bayesian model adequacy and choice in phylogenetics, Mol. Biol. Evol. source
The citation is attached to the general claim about model adequacy and artifactual phylogenetic results, not the citing authors’ conclusion about Porifera-sister. The Introduction states that poorly fitting models can produce erroneous or biased phylogenetic inferences. No page number is provided in our copy. (LLM, conf=0.90)
- Not checked yetcites [18] Heath, 2008, Taxon sampling and the accuracy of phylogenetic analyses, J. Syst. Evol.
- Partly supportedcites [19] Ripplinger, 2010, Assessment of substitution model adequacy using frequentist and Bayesian methods, Mol. Biol. Evol. sourceExperimental — accuracy not yet measured
The citation is attached to the general premise about model adequacy, not to the citing authors’ Porifera-sister conclusion. The Discussion says an appropriate model is important for certain difficult tree shapes, but also reports no correlation between substitution-model adequacy and phylogenetic performance overall. It therefore supports a qualified version of the premise, not the unqualified claim that better-fitting models are generally less likely to recover artifactual topologies. (LLM, conf=0.84)
- Not checked yetcites [20] Ekman, 2011, The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae, Syst. Biol. source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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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
“no routinely used evolutionary model can adequately describe both forms of heterogeneity”
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.
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None of the sources cited for this claim have been checked yet.
In the paper
“We showed that for both datasets, models that have previously been used to study the animal phylogeny fell short, to various degrees, of adequately describing among-site amino acid preferences”
- Also stated in: § SUMMARY · p. 4 · plain
“showing that all models fell short of adequately describing site-specific amino acid preferences”
What the sources say
- Not checked yetcites [21] Whelan, 2001, A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach, Mol. Biol. Evol. source
- Not checked yetcites [22] Le, 2008, An improved general amino acid replacement matrix, Mol. Biol. Evol. source
- Not checked yetcites [23] Yang, 1994, Estimating the pattern of nucleotide substitution, J. Mol. Evol. source
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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- Also stated in: § SUMMARY · p. 4 · 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
“A comparison of the spread of the Z scores obtained, across all models and from all of our PPAs (Tables 1 and S1), indicates that PPA-DIV is more discriminatory: it has a broader distribution of Z scores across models.”
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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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
“Differently, CAT-GTR+G analyses of WhelanD20 recovered either Ctenophora-sister or Porifera-sister (Porifera as the sister group of all other animals) depending on the outgroups used.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the paper
“We show that data-recoding methods [13-15] reduce compositional heterogeneity in these datasets”
What the sources say
- Not checked yetcites [13] Hrdy, 2004, Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I, Nature source
- Not checked yetcites [14] Susko, 2007, On reduced amino acid alphabets for phylogenetic inference, Mol. Biol. Evol. source
- Not checked yetcites [15] Kosiol, 2004, A new criterion and method for amino acid classification, J. Theor. Biol. source
boosteddirect- Asserted: passes — The authors put it forward as true.
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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
“Increased model adequacy is associated with significant topological changes in support of Porifera-sister.”
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“models accommodating site-specific amino acid preferences can better describe the recoded datasets”
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.
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None of the sources cited for this claim have been checked yet.
In the 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”
What the sources say
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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- It may state two separate claims as one. 25
- Probably not a substantial claim. 25
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
“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.”
What the sources say
- Supportedcites [6] Pisani, 2015, Genomic data do not support comb jellies as the sister group to all other animals, Proc. Natl. Acad. Sci. USA source
The cited paper presents both tree topologies under different analytical conditions. In the Results (p. 2), it reports Ctenophora-sister when Fungi is included as a distant outgroup and Porifera-sister under other conditions, while interpreting the former as likely artifactual. (LLM, conf=0.91)
- Supportedcites [7] Simion, 2017, A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals, Curr. Biol. source
The Summary states that several phylogenomic studies supported Porifera-sister, while others recovered Ctenophora-sister. The Introduction likewise describes the two placements in different phylogenomic studies. The supplied passages do not specify page numbers. (LLM, conf=0.94)
- Not checked yetcites [39] Nosenko, 2013, Deep metazoan phylogeny: when different genes tell different stories, Mol. Phylogenet. Evol. source
- Not checked yetcites [41] Philippe, 2009, Phylogenomics revives traditional views on deep animal relationships, Curr. Biol. source
- Supportedcites [42] Pick, 2010, Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships, Mol. Biol. Evol. source
The source supports the Porifera-sister part of the citing sentence. Its Abstract reports that its phylogenomic analysis recovered sponges as sister to all other Metazoa; the sentence cites other studies for Ctenophora-sister. (LLM, conf=0.93)
- Supportedcites [43] Philippe, 2011, Resolving difficult phylogenetic questions: why more sequences are not enough, PLoS Biol. source
This citation is attached to the statement that some studies present both trees, rather than to a claim that this paper's own analyses support both. The Figure 1 caption (Box 2; page unavailable) presents trees from several phylogenomic analyses, while Box 3 describes a Dunn et al. tree placing ctenophores near the outgroup and the paper's reanalysis placing sponges as sister to the other animals. The paper treats the ctenophore placement as a likely artifact, but it does present the competing trees. (LLM, conf=0.86)
- Not checked yetcites [44] Eitel, 2017, A taxogenomics approach uncovers a new genus in the phylum Placozoa, bioRxiv
- Supportedcites [8] Ryan, 2013, The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution, Science source
The Abstract states that the paper’s phylogenomic analyses suggest ctenophores, rather than sponges, are sister to all other animals. The Discussion and Conclusion likewise reports support for Ctenophora-sister, while noting that some analyses also support alternative hypotheses. The source therefore supports the Ctenophora-sister part of the citing sentence. (LLM, conf=0.93)
- Supportedcites [9] Moroz, 2014, The ctenophore genome and the evolutionary origins of neural systems, Nature source
The citation is attached to the Ctenophora-sister part of the sentence. In “Ctenophore phylogeny,” the paper says its analyses place Ctenophora as the most basal animal lineage, which supports that attribution. (LLM, conf=0.93)
- Supportedcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA source
The citation supports the Ctenophora-sister part of the sentence. In “Ctenophores Sister to Other Extant Animals and Monophyletic Sponges,” the paper reports strong support for ctenophores as sister to all other extant animals across its maximum-likelihood and Bayesian analyses. (LLM, conf=0.94)
plaincorrelational- Asserted: passes — The authors put it forward as true.
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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
“Amino acid recoding has long been considered as a powerful strategy to reduce compositional heterogeneity and saturation in the data [7, 13-15, 31-36]”
What the sources say
- Supportedcites [7] Simion, 2017, A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals, Curr. Biol. source
In “Testing the Impact of Compositional Bias,” the paper says it recoded its amino-acid supermatrix using the Dayhoff six-state alphabet to reduce the potential impact of saturation and compositional bias. That supports the cited sentence’s characterization of amino acid recoding as a strategy for addressing those problems. (LLM, conf=0.88)
- Not checked yetcites [13] Hrdy, 2004, Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I, Nature source
- Supportedcites [14] Susko, 2007, On reduced amino acid alphabets for phylogenetic inference, Mol. Biol. Evol. source
The Introduction identifies compositional heterogeneity and saturation as problems for phylogenetic inference and presents amino acid binning as a way to address them. The Discussion reports that binning can correct compositional heterogeneity, while the section “Reduced Alphabets to Adjust for Saturation” explains how it makes sequences less susceptible to multiple substitutions. The paper describes the benefits as dependent on the choice of bins, rather than guaranteed. (LLM, conf=0.84)
- Not checked yetcites [15] Kosiol, 2004, A new criterion and method for amino acid classification, J. Theor. Biol. source
- Not checked yetcites [31] Rodríguez-Ezpeleta, 2007, Detecting and overcoming systematic errors in genome-scale phylogenies, Syst. Biol. source
- Not checked yetcites [32] Cox, 2008, The archaebacterial origin of eukaryotes, Proc. Natl. Acad. Sci. USA source
- Supportedcites [33] Rota-Stabelli, 2013, Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study, Syst. Biol. source
In “Clusters of Taxa With Similar Codon-Usage Bias in the Nucleotide Tree” (p. 10), the paper says Dayhoff amino acid recoding reduces the effects of saturation and compositional bias. “Nucleotides Versus Amino Acids” (p. 1) also describes character recoding as common practice for addressing these problems. (LLM, conf=0.93)
- Supportedcites [34] Domman, 2015, Plastid establishment did not require a chlamydial partner, Nat. Commun. source
In Results and Discussion, under “High levels of compositional heterogeneity in GlgA,” the paper says Dayhoff amino acid recoding greatly reduces substitutional saturation and compositional heterogeneity. It also reports improved model fit after recoding. This supports the cited background statement, though the paper does not itself establish how long the strategy has been considered useful. (LLM, conf=0.93)
- Partly supportedcites [35] Borowiec, 2015, Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa, BMC Genomics sourceExperimental — accuracy not yet measured
The Results and discussion section describes amino acid recoding as an approach shown to reduce the effects of across-taxon compositional heterogeneity. It also reports substantial signal loss and inconsistent topologies in this study. The Methods section assesses saturation separately; our copy does not say recoding reduces saturation. (LLM, conf=0.86)
- Not checked yetcites [36] Schwentner, 2017, A phylogenomic solution to the origin of insects by resolving crustacean-hexapod relationships, Curr. Biol. source
boosteddirect- Asserted: passes — The authors put it forward as true.
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- 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.
- 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
“In contrast, WhelanD20-Holo, the dataset from which fungal outgroups were excluded, and WhelanD20-Choano, the dataset from which all outgroups but the Choanoflagellata were excluded, supported Porifera-sister (PP = 0.68 and PP = 0.77, respectively; Table 3; Figures S2B and S3B).”
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“However, all models, including CAT-GTR+G, were strongly rejected-with the smallest absolute Z score ( j Z j = 12.15) obtained from the CAT-GTR+G analysis of Chang.”
boosted- Asserted: passes — The authors put it forward as true.
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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
“With both tests, CAT-GTR+G obtained the lowest Z scores, and PF-schemes emerged as the second best modeling strategy”
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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In the paper
“Our results show that support for Ctenophora-sister decreases, while at the same time support for Porifera-sister increases, when heterogeneity in the data is better accounted for.”
plaindirect- Asserted: passes — The authors put it forward as true.
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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 recoded datasets obtained lower Z scores than the original amino acid datasets for both PPA-MAX and PPAMEAN (Tables 1 and S1), indicating that recoding is effective at reducing lineage-specific compositional heterogeneity.”
hedgeddirect- Asserted: passes — The authors put it forward as true.
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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 KGB-6, the PP for Porifera-sister was 0.78 for Chang and 0.68 for WhelanD20-Holo.”
plain- Asserted: passes — The authors put it forward as true.
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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
“Under CAT-GTR+G, only PPA-DIV invariably recovered reduced Z scores from the recoded datasets (Table 1), with Z scores from PPA-CONV and PPA-VAR being similar in analyses performed with and without recoding (Table S1).”
plain- Asserted: passes — The authors put it forward as true.
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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
“Similarly, phylogenies inferred from Chang using PF-scheme and CAT-GTR+G (see STAR Methods) supported Ctenophora-sister with 100% bootstrap support and PP z 1, respectively”
plaindirect- Asserted: passes — The authors put it forward as true.
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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
“Support for Ctenophora-sister was severely reduced in CATGTR+Ganalyses of both recoded datasets, with support for Porifera-sister being higher than that for Ctenophora-sister”
plaindirect- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the 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”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA source
- Not checked yetcites [28] Halanych, 2016, Miscues misplace sponges, Proc. Natl. Acad. Sci. USA source
- Not checked yetcites [29] Whelan, 2017, Who let the CAT out of the bag? Accurately dealing with substitutional heterogeneity in phylogenomic analyses, Syst. Biol.
- Not checked yetcites [38] Whelan, 2017, Ctenophore relationships and their placement as the sister group to all other animals, Nat. Ecol. Evol. source
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.
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
“WAG+G, LG+G, GTR+G (with or without recoding), and PF-schemes describe the data worse than CAT-GTR+G and invariably found support for Ctenophora-sister.”
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.
In the paper
“Indeed, a CAT-GTR+G analysis of the Dayhoff-6 recoded version of this dataset reached excellent convergence and found strong support for Porifera-sister (PP = 1; Figure S3K)”
What the sources say
- Not checked yetcites [38] Whelan, 2017, Ctenophore relationships and their placement as the sister group to all other animals, Nat. Ecol. Evol. source
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.
In the paper
“Data recoding reduced the impact of heterogeneity on our phylogenetic analyses (see also [7]), and this lent support to Porifera-sister. Notably, this result emerged independently of the outgroups included.”
What the sources say
- Not checked yetcites [7] Simion, 2017, A large and consistent phylogenomic dataset supports sponges as the sister group to all other animals, Curr. Biol. 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.
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
“Phylogenetic analyses of early animal relationships using models that do not describe site-specific amino acid differences (WAG+G, LG+G, GTR+G, and optimal PF-schemes) invariably support Ctenophora-sister, whereas analyses using models that can accommodate such preferences (e.g., CAT-GTR+G) predominantely favor Porifera-sister.”
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.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our PPA tests indicate that although CAT-GTR+G describes Chang and WhelanD20 better than other models, overall model adequacy can still be improved using data recoding, and Porifera-sister was favored under all recoding strategies.”
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Across-site replacement-pattern heterogeneity [26] and compositional heterogeneity across taxa [13, 55] can both have a misleading effect on phylogenetic reconstruction.”
What the sources say
- Not checked yetcites [26] Lartillot, 2007, Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model, BMC Evol. Biol. source
- Not checked yetcites [13] Hrdy, 2004, Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I, Nature source
- Not checked yetcites [55] Foster, 2004, Modeling compositional heterogeneity, Syst. Biol. source
plainconditional- 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.
None of the sources cited for this claim have been checked yet.
In the 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].”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA source
- Not checked yetcites [6] Pisani, 2015, Genomic data do not support comb jellies as the sister group to all other animals, Proc. Natl. Acad. Sci. USA 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.
None of the sources cited for this claim have been checked yet.
In the paper
“To minimize systematic error, it is important to use the evolutionary model that best fits the data [18, 48-50].”
What the sources say
- Not checked yetcites [18] Heath, 2008, Taxon sampling and the accuracy of phylogenetic analyses, J. Syst. Evol.
- Not checked yetcites [48] Posada, 1998, MODELTEST: testing the model of DNA substitution, Bioinformatics source
- Not checked yetcites [49] Cunningham, 1998, Best-fit maximum-likelihood models for phylogenetic inference: empirical tests with known phylogenies, Evolution
- Not checked yetcites [50] Sullivan, 2005, Model selection in phylogenetics, Annu. Rev. Ecol. Evol. Syst. source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check 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 be too vague to check against evidence.
In the paper
“Shen et al. [11] generated datasets that excluded the few genes that they identified as ''outliers,''”
What the sources say
- Not checked yetcites [11] Shen, 2017, Contentious relationships in phylogenomic studies can be driven by a handful of genes, Nat Ecol Evol 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
“This result rejects the conclusions of [11] that signal for Porifera-sister is limited to ''outlier genes'' and indicates that their approach is model dependent: arguments about model adequacy should be considered when implementing it.”
What the sources say
- Not checked yetcites [11] Shen, 2017, Contentious relationships in phylogenomic studies can be driven by a handful of genes, Nat Ecol Evol 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.
In the 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.”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA 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. It may state two separate claims as one.
In the paper
“GTR+G was used by [8]”
What the sources say
- Not checked yetcites [8] Ryan, 2013, The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution, Science 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.
In the paper
“analyzed these datasets under LG+G, and found support for Ctenophora-sister”
What the sources say
- Not checked yetcites [11] Shen, 2017, Contentious relationships in phylogenomic studies can be driven by a handful of genes, Nat Ecol Evol 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.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“The second is a dataset from [10] that had not been reassessed in [6].”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA source
- Not checked yetcites [6] Pisani, 2015, Genomic data do not support comb jellies as the sister group to all other animals, Proc. Natl. Acad. Sci. USA 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.
In the paper
“WAG+G was used by [9]”
What the sources say
- Not checked yetcites [9] Moroz, 2014, The ctenophore genome and the evolutionary origins of neural systems, Nature source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Branch length is the product of time and substitution rate, and even slowly evolving outgroups can be long branched if they diverged much earlier than the ingroup, potentially exacerbating long-branch attraction artifacts [18, 57].”
What the sources say
- Not checked yetcites [18] Heath, 2008, Taxon sampling and the accuracy of phylogenetic analyses, J. Syst. Evol.
- Not checked yetcites [57] Hillis, 1998, Taxonomic sampling, phylogenetic accuracy, and investigator bias, Syst. Biol. source
plainconditional- 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
“LG+G was used by [11]”
What the sources say
- Not checked yetcites [11] Shen, 2017, Contentious relationships in phylogenomic studies can be driven by a handful of genes, Nat Ecol Evol source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Whelan et al. [38] have increased the number of ctenophoran species compared to those they used in [10].”
What the sources say
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.
In the paper
“Chang was analyzed under its optimal PF-scheme using RAxML version 8.2.9 [63], with support estimated using the rapid bootstrap option (100 replicates).”
What the sources say
- Not checked yetcites [63] Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics 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.
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
“The number of samples to be discarded as burnin was independently assessed for each analysis by visually checking traces of likelihood and parameter values.”
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.
In the paper
“which is very similar to WhelanD20”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA 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.
Probably not a substantial claim.
In the paper
“which apparently explicitly excludes proteins of significant compositional heterogeneity (see [10])”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA source
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.
Probably not a substantial claim.
In the paper
“CAT-GTR+G was used by [6]”
What the sources say
- Not checked yetcites [6] Pisani, 2015, Genomic data do not support comb jellies as the sister group to all other animals, Proc. Natl. Acad. Sci. USA 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.
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
“We conclude that Ctenophora-sister is a tree reconstruction artifact, whereas a placement of the sponges as the sister group of all other animals most likely reflects genuine phylogenetic signal.”
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.
- Rests on an assumption: Ctenophora-sister is currently uncorroborated by independent evidence.
In the paper
“PFschemes were used by [10]”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA 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.
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
“For each analysis two chains were run and convergence was assessed using the bpcomp and tracecomp tools in PhyloBayes.”
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.
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
“All PPA analyses used a minimum of 100 replicates.”
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.
In the paper
“as the latter was obtained in [10] by removing genes of significant compositional heterogeneity from D16”
What the sources say
- Not checked yetcites [10] Whelan, 2015, Error, signal, and the placement of Ctenophora sister to all other animals, Proc. Natl. Acad. Sci. USA 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.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Because amino acids are grouped into classes recoding strategies can in some cases cause signal erosion. This however can be monitored because it will result in collapsed nodes that do not provide support for any topology, rather than a change in the topology supported by the data.”
plainconditional- 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. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Different sites and lineages accumulate substitutions at different rates (e.g., [67-69])”
What the sources say
- Not checked yetcites [67] Yang, 1993, Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites, Mol. Biol. Evol.
- Not checked yetcites [68] Thorne, 1998, Estimating the rate of evolution of the rate of molecular evolution, Mol. Biol. Evol. source
- Not checked yetcites [69] Yang, 1994, Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods, J. Mol. Evol. 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.
None of the sources cited for this claim have been checked yet.
In the paper
“different amino acids are preferentially found at different sites or in different lineages (e.g., [26, 55])”
What the sources say
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.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Because Dayhoff recoding clusters amino acids with comparable properties within the same category, it reduces heterogeneity across both sites and lineages, potentially reducing the impact of systematic errors on phylogenetic estimation under currently available models.”
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. It may state two separate claims as one.
In the paper
“different proteins can have their own protein-specific replacement rates (e.g., [24])”
What the sources say
- Not checked yetcites [24] Lanfear, 2012, Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses, Mol. Biol. Evol. source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“Dayhoff recoding partitions amino acids in six classes or bins (Table 2), based on the log odds matrix of probabilities of pairs of amino acids appearing together in a PAM 250 matrix”
What the sources say
- Not checked yetcites [14] Susko, 2007, On reduced amino acid alphabets for phylogenetic inference, Mol. Biol. Evol. source
- Not checked yetcites [37] Dayhoff, 1978, A model of evolutionary change in proteins
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.
The paper relies on this without support.
Ctenophora-sister is currently uncorroborated by independent evidence.
“whereas Ctenophora-sister is currently uncorroborated by independent evidence”
The authors state this as an assumption.
When computing Z-scores, the null distribution is approximately normal, with the Z-score analogous to a standard normal quantile.
“When computing Z-scores it is assumed that the null distribution is approximately normal, with the Z-score being analogous to a standard normal quantile.”
The paper relies on this without support.
Datasets without outlier genes should not include signal in favor of Porifera-sister.
“As datasets without ''outlier genes'' should not include signal in favor of Porifera-sister”
The paper relies on this without support.
Current implementations of models that explicitly take into consideration across-taxon compositional heterogeneity are computationally too demanding to allow their application to large phylogenomic datasets.
“However, current implementations of these models are computationally too demanding to allow their application to large phylogenomic datasets.”
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 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 RL2 findings also support recent efforts pairing recoding and site-heterogeneous models to resolve difficult, ancient nodes in animal phylogeny5,9,24,33, despite the erosion of data relevant to more shallow nodes.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [9]
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
“By contrast, saturation and convergence are often underestimated when using standard site-homogeneous models, causing LBA8,9,22.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [9]
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
“most current analyses instead find ctenophores to be the sister group either of all other metazoans (Ctenophora-sister hypothesis) or of all animals except sponges (Porifera-sister hypothesis) [4–6, 14”
From Cambrian Sessile, Suspension Feeding Stem-Group Ctenophores and Evolution of the Comb Jelly Body Plan (2019) · cites this paper as [5]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“CAT/CATGTR offers improved resilience to long-branch attraction artefacts (LBA)22 and is almost always better fitting than standard site-homogeneous amino acid substitution models (e.g. WAG)8–10,23–29.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [9]
The cited source says what the claim attributes to it.
In the citing paper
“However, the branch leading to comb jellies is extremely long, and when re-analyses of the same datasets are performed using methods intended to alleviate systematic errors, such as site-heterogeneous models (i.e. CAT/CATGTR) and/or recoding, sponges tend to be recovered as sister to other animals (Fig. 1a)8–10.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [9]
The cited source says what the claim attributes to it.
In the citing paper
“Several studies have already shown that gene family8,71 and unpartitioned phylogenomic analyses using more sophisticated substitution models8–10 reject Ctenophora sister in favour of Porifera sister.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [9]
The cited source says what the claim attributes to it.
In the citing paper
“Despite supporting Ctenophora sister under CATGTR, WEA17 was later shown to support Porifera sister when amino acid recoding strategies and CATGTR are combined, an approach reported to allow better accommodation of systematic error9,24.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [9]
In the citing paper
“The topologies from Chang and Feuda are based on the same data set which is made up of 51,940 amino acid positions from 78 taxa representing a wide range of animals and 9 non-animal outgroups.”
From Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses (2019) · cites this paper as Feuda et al. 2017
In the citing paper
“Feuda extensively applied six-state amino acid recoding to this data set in a reanalysis of the Chang study, which did not use recoding.”
From Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses (2019) · cites this paper as Feuda et al. 2017
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
§ SUMMARY · p. 4
“All recoded datasets obtained lower Z scores than the original amino acid datasets for both PPA-MAX and PPAMEAN (Tables 1 and S1)”
§ SUMMARY · p. 4
“| Dayhoff-6 | GTR | 78.06 | 26.99 |”
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
§ SUMMARY · p. 4
“WhelanD20-Opistho (70 taxa, including all the original outgroups, and 46,542 amino acid positions)”
§ Dataset selection · p. 10
“This dataset scores 70 taxa and 42,542 amino acid positions.”
Citations
Cites
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
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820
Cross validatory choice and assessment of statistical predictions
Stone, M. (1974) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1974.tb00994.x · Cited by 10,881
The rapid generation of mutation data matrices from protein sequences
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A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans
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Metadata
- Authors
- Feuda, R., Dohrmann, M., Pett, W., Philippe, H., Rota-Stabelli, O., Lartillot, N., Wörheide, G., & Pisani, D.
- Affiliations
- California Institute of Technology (US)
- Ludwig-Maximilians-Universität München (DE)
- Iowa State University (US)
- Centre National de la Recherche Scientifique (FR)
- Lyon 1 Université (FR)
- Bayerische Staatssammlung für Paläontologie und Geologie (DE)
- University of Bristol (GB)
- Corresponding author
- Wörheide, Gert
- Pisani, Davide
- Venue
- Current Biology
- Publisher
- Elsevier BV
- Published
- 2017-12
- Volume
- 27
- Issue
- 24
- Pages
- 3864-3870.e4
- ISSN
- 0960-9822 (ISSN-L)
- OpenAlex
- W2775427740
- Semantic Scholar
- c5ee9d8995148b11f400719b18bbe60028a76e97
- Cited by
- 291
- References
- 72
- Citations by year
- 2026: 10 · 2025: 22 · 2024: 25 · 2023: 23 · 2022: 29 · 2021: 49 · 2020: 37 · 2019: 56 · 2018: 40
- FWCI
- 25.85
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Current Biology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Explore Bristol Research (publishedVersion, cc-by)
- CINECA IRIS Institutional Research Information System (Fondazione Edmund Mach) (submittedVersion, cc-by)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
- HAL (submittedVersion)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Iris (University of Trento) (submittedVersion, cc-by)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Funders
- NERC (NE/P013643/1)
- Templeton Foundation (60579)
- French Laboratory of Excellence (ANR-10-LABX- 41, ANR-11-IDEX-0002-02)
- French National Research Agency (ANR-10-BINF-01-01)
- LMU Munich’s Institutional Strategy LMUexcellent
- German Research Foundation (DFG) (Wo896/15-1)
- 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
- animal phylogeny, sponges, comb jellies, Ctenophora, sister group relationships, compositional heterogeneity, data recoding, topology change
- MeSH terms
- Animals, Biological Evolution, Phylogeny, Porifera, Sequence Analysis, Protein
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-06, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-06 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
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 ›
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