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

In the paper

“However, ctenophores were recovered as sister to all other extant animals in maximumlikelihood analyses with greater taxon sampling (Bayesian inference never converged for datasets with more than 19 taxa).”

What the sources say

• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured

In the paper

“For example, Ryan et al. (6) recovered a sister relationship between sponges and ctenophores in analyses where taxa with high amounts of missing data were excluded, and support for this was highest in Bayesian inference with the CAT (17) substitution model.”

What the sources say

• Supported

  In “Phylogenetic position of Mnemiopsis leidyi” (page not available), the Genome Set includes only complete genomes and has substantially less missing data than the EST Set. The paper reports that Bayesian analysis of the Genome Set, using the CAT model, strongly supports a Ctenophora–Porifera clade, whereas maximum-likelihood analyses give it only some support. (LLM, conf=0.91)

  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
• Supported

  Citation (17) identifies the CAT model, not Ryan et al.’s findings. The Background describes CAT as a site-heterogeneous mixture model implemented in a Bayesian framework, and the Results and Discussion compare its use in phylogenetic analyses with WAG. (LLM, conf=0.93)

  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

In the paper

“Additional sources of systematic error include poor taxon or character sampling (10,14,15), large amounts of missing data (16), and model misspecification (16,17).”

What the sources say

• Supported

  This source is cited for poor taxon or character sampling, not for missing data or model misspecification. The paper argues that insufficient taxon sampling produced erroneous phylogenetic results and notes that character-rich analyses are thought to outperform character-poor ones (Abstract; page unavailable in our copy). (LLM, conf=0.91)

  cites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. source
• ?Not checked — no full text of the sourcecites [14] 14. Heath TA, Hedtke SM, Hillis DM (2008) Taxon sampling and the accuracy of phylo- genetic analyses. J Syst Evol 46(3):239-257. source
• ?Not checked — no full text of the sourcecites [15] 15. Jeffroy O, Brinkmann H, Delsuc F, Philippe H (2006) Phylogenomics: The beginning of incongruence? Trends Genet 22(4):225-231. source
• ?Not checked — no full text of the sourcecites [16] 16. Roure B, Baurain D, Philippe H (2013) Impact of missing data on phylogenies inferred from empirical phylogenomic data sets. Mol Biol Evol 30(1):197-214. source
• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured

In the paper

“Other than progressive data filtering, differences between datasets analyzed here and those used in previous studies of basal metazoan relationships (3-10) are increased character sampling and less missing data compared with some studies and increased nonbilaterian taxon sampling.”

What the sources say

• ?Not checked — no full text of the sourcecites [3] 3. Dunn CW, et al. (2008) Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452(7188):745-749. source
• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• Supported

  The citation identifies this paper as a previous study of basal metazoan relationships. Its Ctenophore phylogeny section reports analyses of those relationships, and its Methods describe the datasets used. The claimed improvements belong to the citing authors’ comparison of datasets, not to a finding attributed to this source. (LLM, conf=0.90)

  cites [5] 5. Moroz LL, et al. (2014) The ctenophore genome and the evolutionary origins of neural systems. Nature 510(7503):109-114. source
• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source
• Supported

  The citation identifies this paper as one of the previous studies of basal metazoan relationships, rather than asking it to describe the citing authors’ new dataset. In ‘Issues at the Level of Taxon Sampling,’ the paper compares nonbilaterian sampling across earlier datasets; in ‘Box 3,’ it reports missing-data levels for an updated dataset. Those passages support its role as a prior study in the comparison. (LLM, conf=0.84)

  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
• ?Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
• Partly supported

  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)

  cites [10] 10. Pick KS, et al. (2010) Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships. Mol Biol Evol 27(9):1983-1987. sourceExperimental — accuracy not yet measured

In the paper

“Phylogenomic studies have resulted in controversial hypotheses placing either Placozoa (Fig. 1A) (2), ctenophores (ctenophore-sister hypothesis) (Fig. 1B) (3)(4)(5)(6)(7), or a clade of ctenophores and sponges (Fig. 1C) (6) as sister to all remaining animals.”

What the sources say

• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• ?Not matched

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

  cites (3)(4)(5)(6)(7)
• Supported

  The Phylogenetic position of Mnemiopsis leidyi section (page not supplied) reports substantial support for ctenophores as sister to all other animals. It also reports that a Bayesian analysis strongly supports a ctenophore–sponge clade as sister to the remaining animals, while cautioning that the result may reflect poor taxon sampling. Those are the two hypotheses for which this paper is cited; the Placozoa hypothesis has a different citation. (LLM, conf=0.93)

  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 the paper

“Our robust support of sponge monophyly agrees with morphology (35) and most other large molecular datasets (5,6,(8)(9)(10).”

What the sources say

• ?Not checked — no full text of the sourcecites [35] 35. Ax P (1996) Multicellular Animals: A New Approach to the Phylogenetic Order in Nature (Springer, Berlin). source
• Supported

  The Ctenophore phylogeny section (page unavailable) reports that its molecular analysis recovered Porifera as a group, with 100% bootstrap support. This supports citing the paper as one molecular dataset consistent with sponge monophyly; the separate morphology citation is not attributed to this source. (LLM, conf=0.91)

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

  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)

  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. sourceExperimental — accuracy not yet measured
• Partly supported

  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)

  cites [8] 8. Philippe H, et al. (2011) Resolving difficult phylogenetic questions: Why more se- quences are not enough. PLoS Biol 9(3):e1000602. sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source
• Supported

  The cited paper is one of the molecular datasets invoked by the sentence. Its Abstract reports that its expanded phylogenomic analysis recovered monophyletic Porifera, supporting the claimed agreement on sponge monophyly. (LLM, conf=0.92)

  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 paper

“Ribosomal protein genes have previously been identified as a potential source of phylogenetic error (32)”

What the sources say

• Supported

  The Results and discussion section (page not provided) says that ribosomal proteins might mislead phylogenetic analyses because of evolutionary biases. It also warns that relying on genes from a single macromolecular complex can produce a biased phylogenetic picture. (LLM, conf=0.93)

  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

In the paper

“Notably, a study focused only on myxozoan cnidarians (34) used the same matrix as Philippe et al. ( 9), but added two highly divergent cnidarians and recovered ctenophores sister to all other animals.”

What the sources say

• Partly supported

  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)

  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. sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source

In the paper

“extremely low mutation rates can indicate selection and result in too little phylogenetic information, both of which could lead to the inference of incorrect relationships (33).”

What the sources say

• Partly supported

  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)

  cites [33] 33. Edwards SV (2009) Natural selection and phylogenetic analysis. Proc Natl Acad Sci USA 106(22):8799-8800. sourceExperimental — accuracy not yet measured

In the paper

“Importantly, biases resulting from elevated compositional heterogeneity or elevated substitution rates are ruled out.”

• Also stated in: § Systematic Biases and Their Effect on Phylogenetic Inference. · plain

  “Removing OGs with high amino acid compositional heterogeneity (datasets 7-11, 17-21, 23, and 25 in Fig. 2) also had no effect on branching order (Fig. 3 and Figs.S2 A-E, S3 E and F, S4 A-E, and S5A).”

In the paper

“Placement of ctenophores as sister to all other animals, and sponge monophyly, are strongly supported under multiple analyses, herein.”

• Also stated in: § Ctenophores Sister to Other Extant Animals and Monophyletic Sponges. · boosted

  “All maximum-likelihood analyses with outgroups resulted in topologies with strong support [≥ 97% bootstrap support (BS)] for ctenophores sister to all other extant animal lineages (datasets 1-21 in Figs. 2 and 3 and Figs.S1-S4).”

• Also stated in: § Placement of Ctenophores Sister to all Remaining Animals Is Not · boosted

  “Every analysis conducted herein strongly supported the ctenophore-sister hypothesis (Fig. 3 and Table 1).”

In the paper

“For example, most topologies with both certain and uncertain paralogs removed had strong support for sponge monophyly (i.e., ≥ 95% BS) (datasets 12-14 and 18-20 in Figs. 2 and 3 and Figs.S2F, S3 A, B, and F, and S4 A and B), but four analyses with only certain paralogs removed recovered low support (< 90% BS) for sponge monophyly (datasets 5, 7, 9, and 10 in Figs. 2 and 3 and Figs.S1E and S2 A, D,”

In the paper

“We also find strong support for sponge monophyly in contrast to previous reports (7,(22)(23)(24).”

What the sources say

• ?Not matched

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

  cites (7,(22)(23)(24)

In the paper

“Analyses with all outgroup taxa removed (datasets 22-25 in Fig. 2) recovered identical relationships among major metazoan lineages as other analyses (Figs.S4 D-F and S5A). However, we observed low support for relationships among ctenophores, sponges, and placozoans in these analyses.”

In the paper

“When all outgroups except two choanoflagellates were removed (datasets 5, 11, 15, and 21 in Fig. 2), inferred nonbilaterian relationships were identical as in analyses we performed with full outgroup sampling (datasets 5, 11, 15, and 21 in Figs. 2 and 3 and Figs.S1E, S2E, S3C, and S4C), but support for sponge monophyly decreased.”

In the paper

“However, Bayesian inference (Fig. S5E) recovered sponges as sister to all other metazoans, but support for this and other deep nodes were low (PP ≤ 90).”

In the paper

“Topologies inferred with only the slowest evolving half of OGs assembled here (datasets 6 and 16 in Fig. 2) (i.e., least saturated and least prone to homoplasy; see Fig. S7 for saturation plots) recovered high support for ctenophores sister to all other animals and sponge monophyly with both maximum-likelihood (BS = 100) (Fig. 3 and Figs.S1F and S3D) and Bayesian inference using the CAT-GTR model”

In the paper

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

In the paper

“We found complete congruence in relationships among basal metazoan phyla in trees inferred with (datasets 1, 2, 8, 12, and 18 in Fig. 2) and without (datasets 3-7, 9-11, 13-17, 19-21, and 22-25 in Fig. 2) taxa and genes that had high LB scores, and nodal support for critical nodes showed little variation among analyses (Fig. 3 and Figs.S1-S5).”

In the paper

“The recovered position of ctenophores was identical in analyses with (datasets 1, 2, 8, 12, and 18 in Fig. 2 and Figs.S1 A and B, S2 B and F, and S3F) and without (datasets 3-7, 9-11, 13-17, and 19-25 in Fig. 2, and Figs.S1 C-F, S2 A and C-E, S3 A-E, S4, and S5 A-C) taxa and genes with high LB scores, and analyses with the slowest evolving genes (datasets 6 and 16 in Fig. 2 and Fig. S7) also”

In the paper

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

In the paper

“However, sponge monophyly was recovered in all of our analyses and best supported when the strictest orthology criteria were applied with TreSpEx (Fig. 3 and Table 1), which also removes sequences resulting from sample contamination (e.g., endosymbionts).”

In the paper

“Inaccurate orthology assignment can also introduce systematic error into phylogenomic analyses.”

In the paper

“This lower mutational saturation has been the primary rational for emphasizing ribosomal genes when inferring deep animal relationship (7).”

What the sources say

• ?Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source

In the paper

“Maximum-likelihood and Bayesian inference using the CAT-GTR model of the least saturated datasets (datasets 6 and 16 in Fig. 2 and Fig. S7) recovered identical basal relationships as our other analyses (Fig. 3 and Figs.S1F, S3D, and S5 B and C), also indicating homoplasy and model choice did not bias results.”

In the paper

“Ideally, if robust datasets are assembled and causes of systematic error are accounted for, different datasets and analytical methods will converge on a single phylogenetic hypothesis (19).”

What the sources say

• ?Not checked — no full text of the sourcecites [19] 19. Philippe H, Delsuc F, Brinkmann H, Lartillot N (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36:541-562. source

In the paper

“Nosenko et al. (7) analyzed a dataset without ribosomal protein genes and recovered ctenophores sister to all other animals, but a similar analysis has not been done for the original Philippe et al. (9) dataset.”

What the sources say

• ?Not checked — no full text of the sourcecites [7] 7. Nosenko T, et al. (2013) Deep metazoan phylogeny: When different genes tell dif- ferent stories. Mol Phylogenet Evol 67(1):223-233. source

In the paper

“the above indicates that ctenophores sister to cnidarians as in Philippe et al. ( 9) was caused by either limited cnidarian taxon sampling, misleading signal in ribosomal genes, or both.”

What the sources say

• ?Not checked — no full text of the sourcecites [9] 9. Philippe H, et al. (2009) Phylogenomics revives traditional views on deep animal re- lationships. Curr Biol 19(8):706-712. source

In the paper

“The AU test (31) was used to determine if a priori hypotheses of basal metazoan relationships could be rejected (Fig. 1).”

What the sources say

• ?Not checked — no full text of the sourcecites [31] 31. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51(3):492-508. source

In the paper

“Convergence was also assessed with tracecomp (26) to ensure each parameter had a maximum discrepancy between chains of less than 0.3 and an effective sample size of at least 50.”

What the sources say

• ?Not checked — no full text of the sourcecites [26] 26. Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic re- construction with infinite mixtures of profiles in a parallel environment. Syst Biol 62(4):611-615. source

In the paper

“Phylobayes analyses were run with two chains until the maxdiff statistic between chains was below 0.3 as measured by bpcomp (26).”

What the sources say

• ?Not checked — no full text of the sourcecites [26] 26. Lartillot N, Rodrigue N, Stubbs D, Richer J (2013) PhyloBayes MPI: Phylogenetic re- construction with infinite mixtures of profiles in a parallel environment. Syst Biol 62(4):611-615. source

In the paper

“Furthermore, the Porifera-sister hypothesis lacks critical evaluation and homology of many characters in these taxa still need thorough analysis (44).”

What the sources say

• ?Not checked — no full text of the sourcecites [44] 44. Halanych KM (2015) The ctenophore lineage is older than sponges? That cannot be right! Or can it? J Exp Biol 218(Pt 4):592-597. source

In the paper

“Nodal support was measured with 100 fast bootstrap replicates.”

In the paper

“Computational demands and convergence issues prevented us from using the CAT-GTR+Γ model for most datasets.Therefore, Bayesian phylogenies are only reported for the two analyses of the slowest evolving half of OGs.”