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Cited by 331Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic StudiesProtist diversity and phylogeny

Error, signal, and the placement of Ctenophora sister to all other animals

Open access
Whelan, Nathan V., Kocot, Kevin M., Moroz, Leonid L., Halanych, Kenneth M.·2015·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1503453112PMC PMC4426464
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Abstract

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.

Integrity signals

Registry

Crossref · 10.1073/pnas.1503453112

Cites

60 of 60 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

35 of 80 cited sources checked · 14 supported · 3 flagged · accuracy not yet measured

  • Interpretationown data

    The argument that long-branch attraction or saturated datasets caused past studies to find ctenophores sister to all other animals seems to have been overstated.

    “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.”
    Quote in the paperSubstantial claim2 of 4 sources checked
    • cites [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
    • cites [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 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.

      Experimental — accuracy not yet measured
    • cites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
    • cites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. source

      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.

      Experimental — accuracy not yet measured
  • Interpretationreasoning

    Long-branch attraction plausibly influenced the phylogenetic position of ctenophores in analyses of Ryan et al. that recovered ctenophores-sister.

    “Therefore, LBA plausibly influenced the phylogenetic position of ctenophores in analyses of Ryan et al. (6) that recovered ctenophores-sister.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [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 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.

      Experimental — accuracy not yet measured
  • Findingcitation

    Ribosomal protein genes possess a conflicting signal compared with other genes.

    “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).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [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
  • Premisecitation

    In Moroz et al., 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.

    “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.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. source
  • Findingcitation

    Inferred relationships among major sponge lineages (Demospongiae + Hexactinellida sister to Calcarea + Homoscleromorpha) are consistent with morphology and most other molecular analyses that recovered monophyletic sponges.

    “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).”
    Quote in the paperNot a substantial claim6 of 8 sources checked
    • cites [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
    • cites [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. source

      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)

      Experimental — accuracy not yet measured
    • cites [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. source

      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)

      Experimental — accuracy not yet measured
    • cites [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 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)

      Experimental — accuracy not yet measured
    • cites [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 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)

      Experimental — accuracy not yet measured
    • cites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
    • cites [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
    • cites [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. source

      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)

      Experimental — accuracy not yet measured
  • May combine two claims. 25
  • Classified as probably not a substantial claim. 12
  • The quote only partly states this claim. 2

  • May combine two claims.

    Premisecitation

    In Ryan et al., ctenophores were recovered as sister to all other extant animals in maximum-likelihood analyses with greater taxon sampling, while Bayesian inference never converged for datasets with more than 19 taxa.

    “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).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [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 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)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    Ryan et al. 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 substitution model.

    “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.”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [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
    • cites [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

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

    Premisecitation

    Additional sources of systematic error include poor taxon or character sampling, large amounts of missing data, and model misspecification.

    “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).”
    Quote in the paperSubstantial claim2 of 5 sources checked
    • cites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. source
    • cites [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
    • cites [15] 15. Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: The beginning of incongruence? Trends Genet 22(4):225-231. source
    • cites [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
    • cites [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

      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)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    Differences between the datasets analyzed here and those used in previous studies of basal metazoan relationships include increased character sampling, less missing data compared with some studies, and increased nonbilaterian taxon sampling.

    “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.”
    Quote in the paperNot a substantial claim5 of 8 sources checked
    • cites [3] 3. Dunn CW, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452(7188):745-749. source
    • cites [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. source

      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)

      Experimental — accuracy not yet measured
    • cites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. source
    • cites [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 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)

      Experimental — accuracy not yet measured
    • cites [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
    • cites [8] 8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more se- quences are not enough. PLoS Biol 9(3):e1000602. source
    • cites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
    • cites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. source

      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)

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Phylogenomic studies have resulted in controversial hypotheses placing either Placozoa, ctenophores, or a clade of ctenophores and sponges as sister to all remaining animals.

    “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.”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites [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. source

      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)

      Experimental — accuracy not yet measured
    • cites (3)(4)(5)(6)(7)

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

    • cites [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

  • May combine two claims.

    Interpretationown data

    Our robust support of sponge monophyly agrees with morphology and most other large molecular datasets.

    “Our robust support of sponge monophyly agrees with morphology (35) and most other large molecular datasets (5,6,(8)(9)(10).”
    Quote in the paperNot a substantial claim4 of 6 sources checked
    • cites [35] 35. Ax P (1996) Multicellular Animals: A New Approach to the Phylogenetic Order in Nature (Springer, Berlin). source
    • cites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. source
    • cites [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 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)

      Experimental — accuracy not yet measured
    • cites [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 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)

      Experimental — accuracy not yet measured
    • cites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
    • cites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. source

  • Classified as probably not a substantial claim.

    Premisecitation

    Ribosomal protein genes have previously been identified as a potential source of phylogenetic error.

    “Ribosomal protein genes have previously been identified as a potential source of phylogenetic error (32)”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [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

  • May combine two claims.

    Premisecitation

    A study focused only on myxozoan cnidarians used the same matrix as Philippe et al. but added two highly divergent cnidarians and recovered ctenophores sister to all other animals.

    “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.”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [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. source

      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)

      Experimental — accuracy not yet measured
    • cites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source

  • May combine two claims.

    Premisecitation

    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.

    “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).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [33] 33. Edwards SV (2009) Natural selection and phylogenetic analysis. Proc Natl Acad Sci USA 106(22):8799-8800. source

      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)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    Biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Ctenophores are sister to all other extant animals, and this placement is strongly supported under multiple analyses in this study.

    “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).”
    Quote in the paperSubstantial claim
    • 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.

  • May combine two claims.

    Findingown data

    Most topologies with both certain and uncertain paralogs removed had strong support for sponge monophyly (≥ 95% BS), but four analyses with only certain paralogs removed recovered low support (< 90% BS) for sponge monophyly.

    “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,”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The study finds strong support for sponge monophyly, in contrast to previous reports.

    “We also find strong support for sponge monophyly in contrast to previous reports (7,(22)(23)(24).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites (7,(22)(23)(24)

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Findingown data

    Analyses with all outgroup taxa removed recovered identical relationships among major metazoan lineages as other analyses, but low support for relationships among ctenophores, sponges, and placozoans.

    “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.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    When all outgroups except two choanoflagellates were removed, inferred nonbilaterian relationships were identical to analyses with full outgroup sampling, but support for sponge monophyly decreased.

    “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.”
    Quote in the paperNot a substantial claim

  • May combine two claims. The quote only partly states this claim.

    Findingown data

    Bayesian inference of the Philippe et al. dataset with ribosomal proteins removed recovered sponges as sister to all other metazoans, but support for this and other deep nodes was low (PP ≤ 90).

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Topologies inferred with only the slowest evolving half of orthologous groups recovered high support for sponge monophyly with both maximum-likelihood (BS = 100) and Bayesian inference using CAT-GTR (PP = 1).

    “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”
    Quote in the paperSubstantial claim

  • The quote only partly states this claim.

    Findingown data

    The maximum-likelihood analysis of the Philippe et al. dataset with ribosomal proteins removed recovered strong support for ctenophores as sister to all other metazoan lineages (BS = 93).

    “The maximum-likelihood analysis recovered strong support for ctenophores as sister to all other metazoan lineages (BS = 93) (Fig. S5D).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Relationships among basal metazoan phyla were completely congruent in trees inferred with and without taxa and genes that had high long-branch scores, and nodal support for critical nodes showed little variation among analyses.

    “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).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The recovered position of ctenophores was identical in analyses with and without taxa and genes with high long-branch scores, and analyses with the slowest evolving genes also recovered ctenophores sister to all other animals.

    “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”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Removal of paralogs as identified by TreSpEx appeared to have the greatest effect on support for some critical nodes, although relationships among basal lineages were unaffected.

    “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.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Sponge monophyly was recovered in all of our analyses and best supported when the strictest orthology criteria were applied with TreSpEx.

    “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).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    Inaccurate orthology assignment can introduce systematic error into phylogenomic analyses.

    “Inaccurate orthology assignment can also introduce systematic error into phylogenomic analyses.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Lower mutational saturation has been the primary rationale for emphasizing ribosomal genes when inferring deep animal relationships.

    “This lower mutational saturation has been the primary rational for emphasizing ribosomal genes when inferring deep animal relationship (7).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [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

  • May combine two claims.

    Interpretationown data

    Maximum-likelihood and Bayesian inference using the CAT-GTR model of the least saturated datasets recovered identical basal relationships as other analyses, indicating homoplasy and model choice did not bias results.

    “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.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    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.

    “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).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [19] 19. Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36:541-562. source

  • May combine two claims.

    Premisecitation

    Nosenko et al. analyzed a dataset without ribosomal protein genes and recovered ctenophores sister to all other animals.

    “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.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [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

  • May combine two claims.

    Interpretationreasoning

    Ctenophores sister to cnidarians as in Philippe et al. was caused by either limited cnidarian taxon sampling, misleading signal in ribosomal genes, or both.

    “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.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    The AU test was used to determine if a priori hypotheses of basal metazoan relationships could be rejected.

    “The AU test (31) was used to determine if a priori hypotheses of basal metazoan relationships could be rejected (Fig. 1).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [31] 31. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51(3):492-508. source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductcitation

    Convergence was assessed with tracecomp to ensure each parameter had a maximum discrepancy between chains of less than 0.3 and an effective sample size of at least 50.

    “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.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [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

  • Classified as probably not a substantial claim.

    Study design and conductcitation

    Phylobayes analyses were run with two chains until the maxdiff statistic between chains was below 0.3 as measured by bpcomp.

    “Phylobayes analyses were run with two chains until the maxdiff statistic between chains was below 0.3 as measured by bpcomp (26).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [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

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing). May combine two claims.

    Premisecitation

    The Porifera-sister hypothesis lacks critical evaluation and homology of many characters in these taxa still need thorough analysis.

    “Furthermore, the Porifera-sister hypothesis lacks critical evaluation and homology of many characters in these taxa still need thorough analysis (44).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [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

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Nodal support was measured with 100 fast bootstrap replicates.

    “Nodal support was measured with 100 fast bootstrap replicates.”
    Quote in the paperNot a substantial claim

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

    Study design and conductreasoning

    Computational demands and convergence issues prevented the use of the CAT-GTR+Γ model for most datasets, so Bayesian phylogenies are only reported for the two analyses of the slowest evolving half of OGs.

    “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.”
    Quote in the paperSubstantial claim
34 of 34

  • 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.”
3 of 3

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 primary remaining lines of evidence supporting Ctenophora sister, partitioned phylogenomics and measures of underlying support (such as ΔPSlnl values), do not do so when better-fitting site-heterogeneous models are incorporated into the analysis.

    “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]

    Split into 2 atoms — 0 confirmed, 1 partially supported, 1 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

    Checked by a reasoning model — may be wrong.

    Experimental — accuracy not yet measured

  • The lack of support for Coelenterata and decreased support for Porifera-sister in Whelan et al.'s reanalysis was not caused by the absence of a misleading signal specific to ribosomal proteins, but instead by a bias introduced by distant outgroups that becomes dominant when only the faster evolving nonribosomal proteins are retained.

    “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]

    Split into 2 atoms — 0 confirmed, 0 partially supported, 2 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

    Checked by a reasoning model — may be wrong.

    Experimental — accuracy not yet measured

  • In the Whelan et al. datasets, excluding distantly related outgroups decreased support for Ctenophora-sister and increased support for Porifera-sister under the site-heterogeneous CAT model.

    “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]

    In “Systematic Biases and Their Effect on Phylogenetic Inference” (page unavailable), Whelan et al. report that removing all outgroups except two choanoflagellates left the inferred relationships unchanged and Ctenophora-sister at 100% bootstrap support. The paper reports CAT-GTR analyses for the slowest-evolving datasets, not a CAT comparison showing that outgroup exclusion decreased Ctenophora-sister support or increased Porifera-sister support. (LLM, conf=0.88)

    Checked by a reasoning model — may be wrong.

    Experimental — accuracy not yet measured

  • Studies using partitioned site-homogeneous models have always recovered comb jellies as sister to other animals.

    “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]

    The Abstract and ‘Placement of Ctenophores Sister to all Remaining Animals Is Not Sensitive to Systematic Errors’ section report that all partitioned maximum-likelihood analyses in this paper recovered ctenophores as sister to other animals. They do not establish that studies using partitioned site-homogeneous models have always done so; the paper notes conflicting results among earlier analyses. Page numbers are unavailable in our copy. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Relaxed clustering has previously shown that partitioning by gene is the best fit for the WEA15 dataset.

    “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]

    The Orthology Determination and Data Filtering section says the authors used relaxed clustering in PartitionFinder to select partitioning schemes and then used those schemes for maximum-likelihood analyses. It does not say that partitioning by gene was the best-fitting scheme for the WEA15 dataset. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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.

  • A 90% result is classified as below 90%

    Minor

    Dataset 9 is listed among analyses with less than 90% bootstrap support for sponge monophyly, whereas Table 1 gives it exactly 90 BS.

  • The same dataset IDs are assigned two outgroup schemes

    Minor

    Datasets 5, 11, 15, and 21 are identified as choanoflagellate-only analyses, then cited as analyses with full outgroup sampling.

  • Dataset 11 falls below the stated ctenophore-support threshold

    Minor

    The text says every maximum-likelihood analysis with outgroups gave at least 97% bootstrap support for ctenophores as sister to the other animals. Table 1 reports 92 BS for dataset 11, which retains choanoflagellate outgroups.

  • Table 1 assigns Philippe et al. the wrong reference number

    Minor

    Table 1 labels the Philippe et al. analysis as reference 7, while the reference list identifies reference 7 as Nosenko et al.; Philippe et al. is reference 9.

  • Several alternative-hypothesis P values exceed the claimed bound

    Minor

    The stated upper bound is P ≤ 0.001 for every alternative-hypothesis test, but Table 1 includes P = 0.01 for the Porifera-sister hypothesis in dataset 4. Other entries also exceed the bound.

5 of 5

Cites

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Related

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)
ORCID
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
DOI
10.1073/pnas.1503453112
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
Licence
www.pnas.org/site/misc/userlicense.xhtml (vor)
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
National Aeronautics and Space Administration (NASA-NNX13AJ31G)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › 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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-11.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-11.

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Statistics and arithmetic are recomputed, not judged.

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