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Cited by 702Marine Invertebrate Physiology and EcologyMarine Sponges and Natural ProductsMarine Ecology and Invasive Species

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

Open access
Ryan, Joseph F., Pang, Kevin, Schnitzler, Christine E., Nguyen, Anh-Dao, Moreland, R. Travis, Simmons, David K., Koch, Bernard J., Francis, Warren R. +10 more·2013·Science
DOI 10.1126/science.1242592PMC PMC3920664
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Abstract

An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.

Integrity signals

Registry

Crossref · 10.1126/science.1242592

Cites

52 of 52 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

11 of 35 cited sources checked · 6 supported · 0 flagged · accuracy not yet measured

  • Findingcitation

    Other genes known to be involved in bilaterian mesoderm development, such as gli/glis genes, are expressed in neural but not mesodermal cells in M. leidyi.

    “Other genes known to be involved in bilaterian mesoderm development, such as gli/glis genes, are expressed in neural (but not mesodermal) cells in M. leidyi (47).”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [47] source

      The Results section reports Mlglis and Mlgli expression in putative sensory cells of the M. leidyi apical organ, with Mlglis absent from other tissues; the Abstract describes their expression as exclusively neural. But the Discussion identifies zic genes, not gli/glis genes, as having mesodermal expression throughout Bilateria. The cited paper therefore supports the M. leidyi expression pattern, but not the claim that gli/glis genes are known to be involved in bilaterian mesoderm development. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
  • Findingown data

    Re-analysis of an expanded set of near intron pairs was consistent with these results.

    “Our re-analysis of an expanded set of near intron pairs (37) was also consistent with these results (Fig. S2).”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [37] source
    • cites Fig. S2

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

  • Findingcitation

    Both A. queenslandica and M. leidyi contain orthologs of transcription factors involved in bilaterian and cnidarian neural development, including lhx, bHLH, six, gli, and sox genes.

    “Both A. queenslandica and M. leidyi contain orthologs of transcription factors involved in bilaterian and cnidarian neural development, including lhx (46), bHLH, six, gli, and sox (classes B, C, E, F) genes.”
    Quote in the paperSubstantial claim1 of 1 sources checked
  • Findingown data

    Phylogenomic analyses of amino acid positions and gene content indicate that ctenophores, not sponges, are the sister lineage to all other animals.

    “Our phylogenomic analyses of both amino acid positions and gene content suggests that ctenophores rather than sponges are the sister lineage to all other animals.”
    Quote in the paperSubstantial claim
  • Findingown data

    The level of repetitive sequence in the M. leidyi genome is low to moderate compared to other metazoans.

    “The level of repetitive sequence in the M. leidyi genome is low to moderate, as compared to other metazoans (Tables S3–4)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites Tables S3–4

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

  • May combine two claims. 20
  • Classified as probably not a substantial claim. 7

  • May combine two claims.

    Findingcitation

    The M. leidyi genome contains the RTK family, the TGF-β signaling pathway, and the canonical Wnt signaling pathway.

    “The cell signaling components present in the M. leidyi genome include the RTK family, which predates the origin of Metazoa (40); the TGF-β signaling pathway (33), thought to have evolved in the metazoan common ancestor (39); and the canonical Wnt signaling pathway (34).”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites [40] source
    • cites [33] source
    • cites [34] source

  • May combine two claims.

    Findingcitation

    Two definitive opsin genes are present in M. leidyi but not A. queenslandica, and are expressed in photocytes and putative photosensory cells in the apical sense organ.

    “An exception to this shared pattern with sponges is the presence of two definitive opsin genes in M. leidyi, but not A. queenslandica, that are expressed in photocytes (light producing cells), as well as in putative photosensory cells in the apical sense organ (12).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [12] source

      The 'Mnemiopsis opsin mRNA expression' section reports expression of two opsin homologs in photocytes and the apical sense organ, and the 'Sequence retrieval for opsin phylogeny' section reports no opsin hits in Amphimedon. However, the paper identifies three putative opsin genes in M. leidyi, not two definitive ones; it demonstrates photopigment function for only MleiOpsin2. Page numbers are unavailable in our copy. (LLM, conf=0.88)

      Experimental — accuracy not yet measured

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

    Findingcitation

    The pattern of presence and absence of gene families and signaling pathway components seen in previous studies is consistent with these results.

    “The pattern of presence and absence of gene families and signaling pathway components seen in previous studies is consistent with these results (32–36).”
    Quote in the paperNot a substantial claim4 of 5 sources checked
    • cites [32] source
    • cites [33] source
    • cites [34] source
    • cites [35] source

      The Results (page unavailable) compare the presence of nuclear-receptor subfamilies across ctenophores, sponges and other animals, including receptors identified in previous studies. The Discussion says their limited diversity in ctenophores and sponges provides evidence for those lineages’ early branching. The paper does not address a broader pattern of signaling-pathway components, so it supports only the gene-family part of the attributed claim. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [36] source

      The Discussion’s ParaHoxozoa section (page unavailable) says that the presence and absence of homeodomain gene families supports a clade uniting cnidarians, bilaterians and placozoans, and relates this pattern to previous studies. The paper does not establish a corresponding pattern for signaling-pathway components, so that part of the attributed claim is unsupported. (LLM, conf=0.82)

      Experimental — accuracy not yet measured

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

    Interpretationcitation

    This interpretation is compatible with a recent report that striated musculature evolved independently in bilaterians, cnidarians, and in the ctenophore Euplokamis dunlapae.

    “This interpretation is compatible with a recent report that striated musculature evolved independently in bilaterians, cnidarians, and in the ctenophore Euplokamis dunlapae (49).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [49] source

      The Results and discussion (page not specified) conclude that striated muscles in bilaterians and hydrozoan cnidarians very likely evolved convergently. For the ctenophore, the paper says only that this *may* apply to Euplokamis sp.; it does not identify the species as Euplokamis dunlapae or establish its independent origin. (LLM, conf=0.87)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Findingown data

    No support was found in any of the analyses for Coelenterata, Diploblastica, or Placozoa being the sister lineage to the rest of animals.

    “We found no support in any of these analyses for Coelenterata (Cn, Ct), Diploblastica (Bi,), or Placozoa being the sister lineage to the rest of animals (Tr,) (Table 1; Fig. S1).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Table 1

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

    • cites Fig. S1

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

  • May combine two claims.

    Findingown data

    The genome of Mnemiopsis leidyi has been sequenced, assembled, and annotated.

    “we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi.”
    Quote in the paperSubstantial claim

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

    Findingcitation

    The M. leidyi genome is among the smallest 7% of genomes when compared to those catalogued in the Animal Genome Size Database.

    “The M. leidyi genome is among the smallest 7% of genomes when compared to those catalogued in the Animal Genome Size Database (26)”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [26]

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

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

    Findingnone given

    The average length of an unspliced M. leidyi transcript is 5.8 kilobases.

    “The average length of an unspliced M. leidyi transcript is 5.8 kilobases.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The final assembly consists of 5,100 scaffolds, resulting in 160-fold physical coverage and an N50 of 187 kilobases.

    “The final assembly consists of 5,100 scaffolds, resulting in 160-fold physical coverage and an N50 of 187 kilobases (SOM S3).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The M. leidyi genome encodes 16,545 predicted protein-coding loci, which comprises 58% of the genome.

    “It encodes 16,545 predicted protein-coding loci, which comprises 58% of the genome”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Putative snail genes were identified in T. inconstans and E. dunlapae, and putative GATA genes in five of seven ctenophore species.

    “We were able to identify putative snail genes in T. inconstans and E. dunlapae, and putative GATA genes in five of the seven species.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Branch lengths in the phylogenetic analyses of concatenated protein matrices show M. leidyi branches to be of similar length to those of Drosophila melanogaster, exhibiting high but not extreme amino acid replacement rates.

    “We have found instead that the branch lengths in the phylogenetic analyses of our concatenated protein matrices show M. leidyi branches to be of similar length to those of Drosophila melanogaster, therefore exhibiting high (but not extreme) amino acid replacement rates (Tables S12–13).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Tables S12–13

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

  • May combine two claims.

    Findingown data

    Relatively few components of the Notch pathway are present and many lack key diagnostic domains.

    “Relatively few components of the Notch pathway (Tables S15–16) are present and many of those lack key diagnostic domains.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Tables S15–16

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

  • May combine two claims.

    Findingown data

    There is substantial support for ctenophore as sister group to the rest of animals, though conflict between maximum-likelihood and Bayesian analysis makes it difficult to determine whether Ctenophora or Porifera are the sister group.

    “The conflict between the maximum-likelihood and Bayesian analysis of the amino acid matrix make it difficult to determine from these analyses whether Ctenophora or Porifera are the sister group to the rest of the Metazoa, but there is substantial support for ctenophore as sister group to the rest of animals (Table 1).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Table 1

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

  • May combine two claims.

    Findingown data

    Sponges and ctenophores lack a similar set of synaptic scaffolding genes, all of which are present in cnidarians and bilaterians.

    “sponges and ctenophores lack a similar set of synaptic scaffolding genes (Tables S17–18), all of which are present in cnidarians and bilaterians (Fig. 5).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Tables S17–18

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

    • cites Fig. 5

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

  • May combine two claims.

    Findingown data

    Broad support was recovered for a sister relationship between Cnidaria and Bilateria and for a clade of Placozoa, Cnidaria, and Bilateria.

    “We recovered broad support for a sister relationship between Cnidaria and Bilateria (Cn, Bi) and for a clade of Placozoa, Cnidaria, and Bilateria (Tr, Cn, Bi).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Gene content data supports Ctenophora as the sister group to all other animals and statistically rejects competing hypotheses.

    “With a ctenophore genome in hand, we show that gene content data supports Ctenophora as the sister group to all other animals and statistically reject competing hypotheses.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Major bilaterian antagonists of TGF-β and Wnt pathways are absent, and Wnt/PCP pathway members Flamingo and Strabismus are not present.

    “Notably absent from both the TGF-β and Wnt pathways are the major bilaterian antagonists; members of the Wnt/PCP pathway, such as Flamingo and Strabismus, are not present.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Gene content analysis produced a tree supporting Ctenophora as the sister group to all other animals and rejected all other alternative topologies at the 5% confidence level.

    “The result of this analysis was a tree supporting Ctenophora as the sister group to all other animals (Ct,) (Fig. 4) and the rejection of all other alternative topologies (in Fig. 2) at the 5% confidence level by likelihood-based statistical hypothesis testing (Table S14).”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites Fig. 4

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

    • cites Table S14

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

  • May combine two claims.

    Findingcitation

    Ionotropic glutamate receptors are absent from A. queenslandica but present in transcriptomes of eight other sponges.

    “Ionotropic glutamate receptors are absent from A. queenslandica, but are present in the transcriptomes of eight other sponges (48).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [48]

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

  • May combine two claims.

    Study design and conductown data

    The assembly is both complete and accurately assembled.

    “These numbers suggest that the assembly is both complete and accurately assembled.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisereasoning

    The inconsistency of reports as to the phylogenetic position of ctenophores has made it difficult to evaluate morphological, developmental, and experimental data involving these animals in an evolutionary context, complicating efforts to understand the early evolution of animals.

    “The inconsistency of reports as to the phylogenetic position of ctenophores (Table S1) has made it difficult to evaluate morphological, developmental, and experimental data involving these animals in an evolutionary context, complicating efforts to understand the early evolution of animals.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Table S1

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

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

    Premisenone given

    The phylogenetic relationship of ctenophores to other animals has been a source of long-standing debate.

    “The phylogenetic relationship of ctenophores to other animals has been a source of long-standing debate.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The Bayesian result may be due to poor taxon sampling in the Genome Set.

    “we suspect the result is due to poor taxon sampling in the Genome Set.”
    Quote in the paperSubstantial claim

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

    Interpretationreasoning

    This result is congruent with the structure and inventory of a variety of gene families and signaling pathways, as well as with genes essential to neural and mesodermal cell types.

    “Nevertheless, this result is congruent with the structure and inventory of a variety of gene families and signaling pathways, as well as with genes essential to neural and mesodermal cell types.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    A less elaborate nervous system was present in the metazoan ancestor and was secondarily reduced in placozoans and sponges.

    “This pattern suggests that a less elaborate nervous system was present in the metazoan ancestor and was secondarily reduced in placozoans and sponges.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    Within ctenophores, the majority of absences are not specific to the M. leidyi lineage, but there are some differences in gene content between ctenophores.

    “These results indicate that, within ctenophores, the majority of absences are not specific to the M. leidyi lineage, but also that there are some intriguing differences in gene content between ctenophores”
    Quote in the paperSubstantial claim
27 of 27

  • The paper relies on this without support.

    Ctenophore biology is critical for reconstructing events that occurred early in animal evolution.

    “An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution.”

  • The paper relies on this without support.

    Sponges lack a nervous system.

    “the sponge A. queenslandica, an animal without a nervous system.”
2 of 2

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?

  • 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.”

    From Error, signal, and the placement of Ctenophora sister to all other animals (2015) · cites this paper as [6]

    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

  • Under the ctenophore-sister scenario, these genes are most parsimoniously interpreted as arising on the myriazoan stem after the divergence of ctenophores, and include genes associated with neuronal function, development and cell adhesion.

    “Under the ctenophore-sister scenario, these are most parsimoniously interpreted as arising on the myriazoan stem after the divergence of ctenophores1,5,59, and include genes associated, in bilaterians and cnidarians, with neuronal function1,5,59, development58 and cell adhesion60.”

    From Ancient gene linkages support ctenophores as sister to other animals (2023) · cites this paper as [1]

    The Phylogenetic position section supports the ctenophore-sister scenario, and Neural components in Mnemiopsis leidyi describes neuronal genes present in cnidarians and bilaterians but absent from ctenophores. It does not establish that these genes as a group arose specifically on the myriazoan stem; the neural-gene passage also reports their absence in sponges. In the printed sentence, development and cell adhesion have separate citations, so those portions are not attributed to this paper. (LLM, conf=0.79)

    Experimental — accuracy not yet measured

  • Recent molecular phylogenies consistently group ctenophores as unrelated to cnidarians with a branching near the basis of the animal tree, but their definite position remains highly debated.

    “Recent molecular phylogenies consistently group ctenophores as unrelated to cnidarians with a branching near the basis of the animal tree, but their definite position remains highly debated (Fig. 1b) (Dunn et al. 2008; Ryan et al. 2013; Simion et al. 2017; Whelan et al. 2015).”

    From A non-bilaterian perspective on the development and evolution of animal digestive systems (2019) · cites this paper as Ryan et al. 2013

    The introductory phylogenetic discussion (page not supplied) describes basal placements of ctenophores and uncertainty about their precise position. But it also reports a phylogenomic study supporting Coelenterata, which groups ctenophores with cnidarians. Thus the source does not support the claim that recent molecular phylogenies *consistently* separate them. (LLM, conf=0.85)

    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 [3]

    The Methods (page unavailable) describe maximum-likelihood analyses using GTR+Γ, and the Phylogenetic position section reports substantial support for ctenophores as sister to other animals. The copy does not identify those analyses as partitioned or establish that studies using partitioned site-homogeneous models have *always* recovered that placement; it also reports an alternative result from a Bayesian analysis. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • 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.”

    From Error, signal, and the placement of Ctenophora sister to all other animals (2015) · cites this paper as [6]

    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

Flagged first, then by citations

1 of the 53 references couldn’t be matched to a known paper.

Research works printed but not linked: 1

  1. Reverberi G., Ortolani G., On the origin of the ciliated plates and mesoderm in the Ctenophore. Acta Embryol. Morphol. Exp. 6, 175–199 (1963).

Cited by

Sorted by citations

Related

Authors
Ryan, J. F., Pang, K., Schnitzler, C. E., Nguyen, A.-D., Moreland, R. T., Simmons, D. K., Koch, B. J., Francis, W. R., Havlak, P., Program, N. C. S., Smith, S. A., Putnam, N. H., Haddock, S. H. D., Dunn, C. W., Wolfsberg, T. G., Mullikin, J. C., Martindale, M. Q., & Baxevanis, A. D.
Affiliations
  • National Institutes of Health (US)
  • University of Bergen (NO)
  • University of Florida (US)
  • Monterey Bay Aquarium Research Institute (US)
  • Rice University (US)
  • Brown University (US)
Corresponding author
Baxevanis, Andreas D.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2013-12-13
Volume
342
Issue
6164
Pages
1242592-1242592
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.1242592
PMC
PMC3920664
OpenAlex
W2164026798
Cited by
702
References
53
Citations by year
2026: 20 · 2025: 34 · 2024: 48 · 2023: 24 · 2022: 46 · 2021: 35 · 2020: 37 · 2019: 55 · 2018: 58 · 2017: 49 · 2016: 75 · 2015: 111 · 2014: 71 · 2013: 1 · 2012: 1
FWCI
111.89
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Rice Research Repository (Rice University) (acceptedVersion)
  • Europe PMC (PubMed Central) (submittedVersion)
  • PubMed Central (submittedVersion)
  • Rice Research Repository (Rice University) (submittedVersion)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Marine Invertebrate Physiology and Ecology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Marine Sponges and Natural Products
  • Physical Sciences › Environmental Science › Global and Planetary Change › Marine Ecology and Invasive Species
Keywords
Mnemiopsis leidyi, ctenophores, genome assembly, genome annotation, phylogenomics, animal evolution, cell type evolution, mesoderm
MeSH terms
Animals, Base Sequence, Biological Evolution, Mesoderm, Molecular Sequence Data

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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.

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