New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

Journal name:
Nature
Volume:
530,
Pages:
94–97
Date published:
DOI:
doi:10.1038/nature16545
Received
Accepted
Published online

The discovery of four new Xenoturbella species from deep waters of the eastern Pacific Ocean is reported here. The genus and two nominal species were described from the west coast of Sweden1, 2, but their taxonomic placement remains unstable3, 4. Limited evidence placed Xenoturbella with molluscs5, 6, but the tissues can be contaminated with prey7, 8. They were then considered deuterostomes9, 10, 11, 12, 13. Further taxon sampling and analysis have grouped Xenoturbella with acoelomorphs (=Xenacoelomorpha) as sister to all other Bilateria (=Nephrozoa)14, 15, or placed Xenacoelomorpha inside Deuterostomia with Ambulacraria (Hemichordata + Echinodermata)16. Here we describe four new species of Xenoturbella and reassess those hypotheses. A large species (>20 cm long) was found at cold-water hydrocarbon seeps at 2,890 m depth in Monterey Canyon and at 1,722 m in the Gulf of California (Mexico). A second large species (~10 cm long) also occurred at 1,722 m in the Gulf of California. The third large species (~15 cm long) was found at ~3,700 m depth near a newly discovered carbonate-hosted hydrothermal vent in the Gulf of California. Finally, a small species (~2.5 cm long), found near a whale carcass at 631 m depth in Monterey Submarine Canyon (California), resembles the two nominal species from Sweden. Analysis of whole mitochondrial genomes places the three larger species as a sister clade to the smaller Atlantic and Pacific species. Phylogenomic analyses of transcriptomic sequences support placement of Xenacoelomorpha as sister to Nephrozoa or Protostomia.

At a glance

Figures

  1. New species of Xenoturbella.
    Figure 1: New species of Xenoturbella.

    a, X. monstrosa (arrows) in a field of A. diagonalis (Ad) and Ectenagena elongata (Ee) clams at 2,890 m depth in Monterey Bay, California. Scale estimated from the average size of A. diagonalis27. b, X. monstrosa (arrow at upper left) and X. churro (asterisk at lower right) at 1,722 m depth near a methane seep in the Guaymas Basin, Mexico. Red spots (lasers) are 29 cm apart. Shell fragments in sediment, but no living clams observed in vicinity. Both specimens contained C. pacifica DNA in their tissues. c, X. profunda female in an A. gigas (Ag) clam field near a carbonate-hosted hydrothermal vent at ~3,700 m depth in Pescadero Basin, Mexico. d. X. hollandorum on sediment adjacent to whale bones (b). Abbreviations: a, anterior; rf, ring furrow; h, hemichordate; o, bone-eating Osedax worms; p, polynoid scaleworm; s, shrimp.

  2. Phylogeny of Xenoturbella based on mitochondrial genomic DNA sequences (15,532 base-pair alignment) using RAxML and GTR + Γ.
    Figure 2: Phylogeny of Xenoturbella based on mitochondrial genomic DNA sequences (15,532 base-pair alignment) using RAxML and GTR + Γ.

    Support assessed via 100 pseudo-replicates of bootstrapping. Scale bar, substitutions per nucleotide position. All nodes were highly supported as indicated by bootstrap support of 100% (asterisk). Rooting based on the topology recovered from the analysis of mitogenomes of Metazoa (Extended Data Fig. 7). Scale bar, substitutions per nucleotide position.

  3. Maximum likelihood phylogeny of animals based on 1,178 genes (394,818 amino acids) with 70% average gene occupancy.
    Figure 3: Maximum likelihood phylogeny of animals based on 1,178 genes (394,818 amino acids) with 70% average gene occupancy.

    Within Bilateria (B), Xenacoelomorpha is sister group to Nephrozoa (N), which includes Protostomia and Deuterostomia. Key nodes were highly supported, as indicated by bootstrap support of 100% (asterisks). Data were analysed using RAxML with GTR, LG and WAG models, + Γ. Support values of less than 100 are shown for GTR + Γ; the same nodes had higher support with LG + Γ and WAG + Γ. Scale bar, substitutions per amino-acid position.

  4. X. monstrosa sp. nov.
    Extended Data Fig. 1: X. monstrosa sp. nov.

    a, Photograph taken by ROV of a vesicomyid clam field at ~3,000 m depth, Monterey Bay, California. Most clams are E. extenta. Two specimens of Xenoturbella are visible (arrows). Scale bar estimated from size of E. extenta (5 cm average width). b, Supplementary Video 1 frame grab showing same clam field as a with A. diagonalis (Ad) and E. extenta clams. Numerous Xenoturbella (arrows) were observed, including two specimens sampled for this study. Scale bar estimated from size of E. extenta (5 cm average width). c, Ventral view of the holotype SIO-BIC BI1037. Although highly contracted and incomplete (the posterior end was removed and frozen and the ventral area removed for histology), the specimen is still over 10 cm long. The mouth (m), ring furrow (rf) and side furrow (sf) are visible. d, Frame grab of paratype SIO-BIC BI1039, a female in situ. e, Dorsal view of paratype SIO-BIC BI1039 (relaxed) showing ring furrow (rf), side furrow (sf), oocytes in body wall (oo) and part of the ventral surface (v). f, Ventral view of paratype SIO-BIC BI1039 showing the mouth (m), ring furrow (rf), oocytes in body wall (oo) and part of the epidermal ventral glandular network (vgn). g, Close-up of the ventral posterior of paratype SIO-BIC BI1039 showing the trailing off of the ventral glandular network (vgn) and oocytes clearly visible in the body wall. h, Close-up of the ventral anterior of paratype SIO-BIC BI1039 showing the mouth (m), ring furrow (rf) and the beginning of the ventral glandular network (vgn) near the anterior tip of the animal.

  5. X. churro sp. nov.
    Extended Data Fig. 2: X. churro sp. nov.

    a, Frame grab of holotype SIO-BIC BI1040, a female, from the Guaymas Transform Fault, Gulf of California, Mexico, at ~1,700 m depth in situ. The ring furrow (rf) is visible towards the anterior end. b, Ventral view of the holotype SIO-BIC BI1040, (relaxed) showing mouth (m), ring furrow (rf), oocytes (oo), side furrow (sf) and epidermal ventral glandular network (vgn). Part of the dorsal side (d) is visible. c, Dorsal view of paratype SIO-BIC BI1039 showing ring furrow (rf) and oocytes (oo). d, Close-up of the ventral posterior of the holotype, showing the trailing off of the ventral glandular network (vgn), oocytes and the distinctively tapering posterior tip. e, Close-up of the anterior end of the holotype, showing the mouth (m), ring furrow (rf) and the beginning of the ventral glandular network (vgn) near the anterior tip of the animal.

  6. X. profunda sp. nov.
    Extended Data Fig. 3: X. profunda sp. nov.

    a, Frame grab of paratype SIO-BIC BI1044, a female, from the Pescadero Basin, Gulf of California, Mexico, at ~3,700 m depth in situ. The ring furrow (rf) is visible towards the anterior end. b, Ventral view of the holotype SIO-BIC BI1041, a male (relaxed) showing mouth (m), ring furrow (rf), side furrow (sf) and epidermal ventral glandular network (vgn). c, Dorsal view of the holotype showing the ring furrow (rf). The ventral glandular network (vgn) is visible where part of the ventral side is exposed. d, Close-up of the ventral anterior end of female paratype SIO-BIC BI1044, showing mouth (m), ring furrow (rf), side furrow (sf) and beginning of ventral glandular network (vgn) near the anterior tip of the animal. e, Close-up of the dorsal posterior of female paratype SIO-BIC BI1044, showing oocytes of different sizes distributed in the parenchyma. f, Parasagittal section (1 μm, stained with toluidine blue) through dorsal body of female paratype SIO-BIC BI1044 showing thick epidermis (e), subepidermal nerve net (n), basal lamina (bl), circular muscle layer (cm), longitudinal muscle layer (lm) and parenchyma with oocytes of various sizes (oo). The gastrodermis is not shown here. g, Parasagittal section (1 μm, stained with toluidine blue) through dorsal body wall of the male holotype SIO-BIC BI1041. Tissue layers as in the female, but a layer of developing (sp.) and mature sperm (s) instead of oocytes is present. The gastrodermis (g) lies beneath the parenchyma layer. h, Parasagittal section (1 μm, stained with toluidine blue) showing parenchyma layer with late spermatids or mature sperm with spherical heads and free flagella.

  7. X. hollandorum sp. nov.
    Extended Data Fig. 4: X. hollandorum sp. nov.

    a, Dorsal view of the live unrelaxed holotype SIO-BIC BI1036, showing ring furrow (rf). b, Ventral view of the holotype (relaxed) showing mouth (m), ring furrow (rf) side furrow (sf) and epidermal ventral glandular network (vgn). c, Close-up of the anterior end of the holotype, showing mouth (m), ring furrow (rf), side furrow (sf) and the ventral glandular network (vgn) near the anterior tip of the animal. d, Close-up of the diamond-shaped mouth.

  8. Mitochondrial COI haplotype networks.
    Extended Data Fig. 5: Mitochondrial COI haplotype networks.

    a, X. bocki and X. westbladi haplotypes (GenBank accession numbers indicated). Sequences from the two nominal species are completely interconnected. This network suggests that there is only one species in Swedish waters, which should be recognized under the older name, X. bocki. b, X. monstrosa from Monterey Bay (California) and Gulf of California (Mexico) (SIO-BIC accession numbers indicated). c, X. profunda from the vicinity of a hydrothermal vent at 3,700 m in the Pescadero Basin, Mexico (SIO-BIC and UNAM specimens indicated). Holotypes are designated with asterisks in the figure. Networks generated with TCS33.

  9. Mitochondrial genomics of Xenoturbella.
    Extended Data Fig. 6: Mitochondrial genomics of Xenoturbella.

    a, Gene order for the four new species compared with that of X. bocki9, 18. The gene order was consistent across all species with only minor variation in amino acids and length of the control region (also see Supplementary Table 1).

  10. Maximum likelihood phylogeny based on all 13 mitochondrial proteins.
    Extended Data Fig. 7: Maximum likelihood phylogeny based on all 13 mitochondrial proteins.

    Five Xenoturbella species formed a weakly supported sister clade to Acoela = Xenacoelomorpha. Xenacoelomorpha was sister to deuterostomes with weak support. Data were partitioned and analysed using RAxML and GTR + Γ. Analysis using PhyloBayes under CAT + GTR + Γ placed Xenacoelomorpha inside deuterostomes as a weakly supported sister group to Chordata (not shown), a result not recovered previously16 with the same program, model and terminals (except for X. profunda). Scale bar, substitutions per amino-acid position. The lower support for Xenacoelomorpha in its placement with deuterostomes, or its placement with Chordata, compared with previously shown, may be due to additional Xenoturbella data and/or the fact that all 13 mitochondrial proteins were used here.

  11. Species tree based on 393 gene trees using Astral II.
    Extended Data Fig. 8: Species tree based on 393 gene trees using Astral II22.

    Nodal support assessed via 100 pseudo-replicates of bootstrapping for each gene, combining both information from each gene tree and its respective bootstrap replicates. B, Bilateria; N, Nephrozoa.

  12. PhyloBayes analysis of 1,178 genes with 70% average gene occupancy.
    Extended Data Fig. 9: PhyloBayes analysis of 1,178 genes with 70% average gene occupancy.

    CAT + GTR + Γ was used and the first 2,000 out of 4,460 generations for two chains were discarded as burn-in and the remainder used to generate a consensus tree. Scale bar, substitutions per amino-acid position. The largest discrepancy observed between chains was 0.164609 and the mean was 0.000989. Xenacoelomorpha grouped with protostomes. B, Bilateria.

  13. Maximum likelihood analyses of ‘fast’- and ‘slow’-evolving data sets.
    Extended Data Fig. 10: Maximum likelihood analyses of ‘fast’- and ‘slow’-evolving data sets.

    The 70% occupancy data set was reduced to 1,127 genes (51 ribosomal proteins removed) and then divided into the fastest-evolving 50% and the slowest-evolving 50%. These were analysed using the PROTGAMMAGTR amino-acid substitution model in RAxML. a, Phylogeny based on the ‘fast-evolving’ data set with 216,066 amino acids. b, Phylogeny based on the ‘slow-evolving’ data set with 168,571 amino acids. Nodal support assessed via 100 pseudo-replicates of bootstrapping. Asterisks indicate 100% bootstrap support. B, Bilateria; N, Nephrozoa.

Videos

  1. Clam field at ~3,000 metres depth Monterey Bay, California.
    Video 1: Clam field at ~3,000 metres depth Monterey Bay, California.
    ROV Tiburon dive 610, October 25, 2004. Collection of a X. monstrosa specimen (type) and images of other Xenoturbella in a field of vesicomyids (mainly Archivesica diagonalis in this clip).
  2. Near Pinkie’s Vent at ~1,700 m depth, a cold-water seep in the Guaymas Transform Fault, Gulf of California, Mexico.
    Video 2: Near Pinkie’s Vent at ~1,700 m depth, a cold-water seep in the Guaymas Transform Fault, Gulf of California, Mexico.
    ROV Doc Ricketts dive 385, April 13, 2012. The Mexican paratype of X. monstrosa is shown initially followed by the holotype of X. churro and then the collection of both specimens.
  3. Sediment near a hydrothermal vent at ~3,700 metres in the Pescadero Basin, Gulf of California, Mexico.
    Video 3: Sediment near a hydrothermal vent at ~3,700 metres in the Pescadero Basin, Gulf of California, Mexico.
    ROV Doc Ricketts dive 757, April 24, 2015. The video shows the female paratype of X. profunda gliding over the sediment in an S-pattern amongst polynoid scaleworms, sea anemones and vesicomyid clams. The video is speeded up to x6 times.

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Author information

Affiliations

  1. Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92037, USA

    • Greg W. Rouse,
    • Nerida G. Wilson &
    • Jose I. Carvajal
  2. Western Australian Museum, Locked Bag 49, Welshpool DC, Western Australia 6986, Australia

    • Nerida G. Wilson
  3. School of Animal Biology, University of Western Australia, Crawley, Western Australia 6009, Australia

    • Nerida G. Wilson
  4. Monterey Bay Aquarium and Research Institute, Moss Landing, California 95039, USA

    • Robert C. Vrijenhoek

Contributions

G.W.R., N.G.W. and R.C.V. collected the specimens. N.G.W. and J.I.C. generated and assembled mitochondrial data for the new Xenoturbella species. J.I.C. generated the Xenoturbella Illumina transcriptome and assembled the data. G.W.R. and J.I.C. performed phylogenetic analyses of mitochondrial genomes and transcriptome data. G.W.R. analysed the morphology of Xenoturbella spp. for the taxonomic descriptions. G.W.R. drafted the paper with J.I.C., N.G.W. and R.C.V. All authors commented on the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to:

Sequence data have been deposited in GenBank; accession numbers can be found in Supplementary Tables 3–5.

Author details

Extended data figures and tables

Extended Data Figures

  1. Extended Data Figure 1: X. monstrosa sp. nov. (956 KB)

    a, Photograph taken by ROV of a vesicomyid clam field at ~3,000 m depth, Monterey Bay, California. Most clams are E. extenta. Two specimens of Xenoturbella are visible (arrows). Scale bar estimated from size of E. extenta (5 cm average width). b, Supplementary Video 1 frame grab showing same clam field as a with A. diagonalis (Ad) and E. extenta clams. Numerous Xenoturbella (arrows) were observed, including two specimens sampled for this study. Scale bar estimated from size of E. extenta (5 cm average width). c, Ventral view of the holotype SIO-BIC BI1037. Although highly contracted and incomplete (the posterior end was removed and frozen and the ventral area removed for histology), the specimen is still over 10 cm long. The mouth (m), ring furrow (rf) and side furrow (sf) are visible. d, Frame grab of paratype SIO-BIC BI1039, a female in situ. e, Dorsal view of paratype SIO-BIC BI1039 (relaxed) showing ring furrow (rf), side furrow (sf), oocytes in body wall (oo) and part of the ventral surface (v). f, Ventral view of paratype SIO-BIC BI1039 showing the mouth (m), ring furrow (rf), oocytes in body wall (oo) and part of the epidermal ventral glandular network (vgn). g, Close-up of the ventral posterior of paratype SIO-BIC BI1039 showing the trailing off of the ventral glandular network (vgn) and oocytes clearly visible in the body wall. h, Close-up of the ventral anterior of paratype SIO-BIC BI1039 showing the mouth (m), ring furrow (rf) and the beginning of the ventral glandular network (vgn) near the anterior tip of the animal.

  2. Extended Data Figure 2: X. churro sp. nov. (543 KB)

    a, Frame grab of holotype SIO-BIC BI1040, a female, from the Guaymas Transform Fault, Gulf of California, Mexico, at ~1,700 m depth in situ. The ring furrow (rf) is visible towards the anterior end. b, Ventral view of the holotype SIO-BIC BI1040, (relaxed) showing mouth (m), ring furrow (rf), oocytes (oo), side furrow (sf) and epidermal ventral glandular network (vgn). Part of the dorsal side (d) is visible. c, Dorsal view of paratype SIO-BIC BI1039 showing ring furrow (rf) and oocytes (oo). d, Close-up of the ventral posterior of the holotype, showing the trailing off of the ventral glandular network (vgn), oocytes and the distinctively tapering posterior tip. e, Close-up of the anterior end of the holotype, showing the mouth (m), ring furrow (rf) and the beginning of the ventral glandular network (vgn) near the anterior tip of the animal.

  3. Extended Data Figure 3: X. profunda sp. nov. (1,421 KB)

    a, Frame grab of paratype SIO-BIC BI1044, a female, from the Pescadero Basin, Gulf of California, Mexico, at ~3,700 m depth in situ. The ring furrow (rf) is visible towards the anterior end. b, Ventral view of the holotype SIO-BIC BI1041, a male (relaxed) showing mouth (m), ring furrow (rf), side furrow (sf) and epidermal ventral glandular network (vgn). c, Dorsal view of the holotype showing the ring furrow (rf). The ventral glandular network (vgn) is visible where part of the ventral side is exposed. d, Close-up of the ventral anterior end of female paratype SIO-BIC BI1044, showing mouth (m), ring furrow (rf), side furrow (sf) and beginning of ventral glandular network (vgn) near the anterior tip of the animal. e, Close-up of the dorsal posterior of female paratype SIO-BIC BI1044, showing oocytes of different sizes distributed in the parenchyma. f, Parasagittal section (1 μm, stained with toluidine blue) through dorsal body of female paratype SIO-BIC BI1044 showing thick epidermis (e), subepidermal nerve net (n), basal lamina (bl), circular muscle layer (cm), longitudinal muscle layer (lm) and parenchyma with oocytes of various sizes (oo). The gastrodermis is not shown here. g, Parasagittal section (1 μm, stained with toluidine blue) through dorsal body wall of the male holotype SIO-BIC BI1041. Tissue layers as in the female, but a layer of developing (sp.) and mature sperm (s) instead of oocytes is present. The gastrodermis (g) lies beneath the parenchyma layer. h, Parasagittal section (1 μm, stained with toluidine blue) showing parenchyma layer with late spermatids or mature sperm with spherical heads and free flagella.

  4. Extended Data Figure 4: X. hollandorum sp. nov. (304 KB)

    a, Dorsal view of the live unrelaxed holotype SIO-BIC BI1036, showing ring furrow (rf). b, Ventral view of the holotype (relaxed) showing mouth (m), ring furrow (rf) side furrow (sf) and epidermal ventral glandular network (vgn). c, Close-up of the anterior end of the holotype, showing mouth (m), ring furrow (rf), side furrow (sf) and the ventral glandular network (vgn) near the anterior tip of the animal. d, Close-up of the diamond-shaped mouth.

  5. Extended Data Figure 5: Mitochondrial COI haplotype networks. (363 KB)

    a, X. bocki and X. westbladi haplotypes (GenBank accession numbers indicated). Sequences from the two nominal species are completely interconnected. This network suggests that there is only one species in Swedish waters, which should be recognized under the older name, X. bocki. b, X. monstrosa from Monterey Bay (California) and Gulf of California (Mexico) (SIO-BIC accession numbers indicated). c, X. profunda from the vicinity of a hydrothermal vent at 3,700 m in the Pescadero Basin, Mexico (SIO-BIC and UNAM specimens indicated). Holotypes are designated with asterisks in the figure. Networks generated with TCS33.

  6. Extended Data Figure 6: Mitochondrial genomics of Xenoturbella. (336 KB)

    a, Gene order for the four new species compared with that of X. bocki9, 18. The gene order was consistent across all species with only minor variation in amino acids and length of the control region (also see Supplementary Table 1).

  7. Extended Data Figure 7: Maximum likelihood phylogeny based on all 13 mitochondrial proteins. (232 KB)

    Five Xenoturbella species formed a weakly supported sister clade to Acoela = Xenacoelomorpha. Xenacoelomorpha was sister to deuterostomes with weak support. Data were partitioned and analysed using RAxML and GTR + Γ. Analysis using PhyloBayes under CAT + GTR + Γ placed Xenacoelomorpha inside deuterostomes as a weakly supported sister group to Chordata (not shown), a result not recovered previously16 with the same program, model and terminals (except for X. profunda). Scale bar, substitutions per amino-acid position. The lower support for Xenacoelomorpha in its placement with deuterostomes, or its placement with Chordata, compared with previously shown, may be due to additional Xenoturbella data and/or the fact that all 13 mitochondrial proteins were used here.

  8. Extended Data Figure 8: Species tree based on 393 gene trees using Astral II22. (199 KB)

    Nodal support assessed via 100 pseudo-replicates of bootstrapping for each gene, combining both information from each gene tree and its respective bootstrap replicates. B, Bilateria; N, Nephrozoa.

  9. Extended Data Figure 9: PhyloBayes analysis of 1,178 genes with 70% average gene occupancy. (225 KB)

    CAT + GTR + Γ was used and the first 2,000 out of 4,460 generations for two chains were discarded as burn-in and the remainder used to generate a consensus tree. Scale bar, substitutions per amino-acid position. The largest discrepancy observed between chains was 0.164609 and the mean was 0.000989. Xenacoelomorpha grouped with protostomes. B, Bilateria.

  10. Extended Data Figure 10: Maximum likelihood analyses of ‘fast’- and ‘slow’-evolving data sets. (132 KB)

    The 70% occupancy data set was reduced to 1,127 genes (51 ribosomal proteins removed) and then divided into the fastest-evolving 50% and the slowest-evolving 50%. These were analysed using the PROTGAMMAGTR amino-acid substitution model in RAxML. a, Phylogeny based on the ‘fast-evolving’ data set with 216,066 amino acids. b, Phylogeny based on the ‘slow-evolving’ data set with 168,571 amino acids. Nodal support assessed via 100 pseudo-replicates of bootstrapping. Asterisks indicate 100% bootstrap support. B, Bilateria; N, Nephrozoa.

Supplementary information

Video

  1. Video 1: Clam field at ~3,000 metres depth Monterey Bay, California. (17.03 MB, Download)
    ROV Tiburon dive 610, October 25, 2004. Collection of a X. monstrosa specimen (type) and images of other Xenoturbella in a field of vesicomyids (mainly Archivesica diagonalis in this clip).
  2. Video 2: Near Pinkie’s Vent at ~1,700 m depth, a cold-water seep in the Guaymas Transform Fault, Gulf of California, Mexico. (27.22 MB, Download)
    ROV Doc Ricketts dive 385, April 13, 2012. The Mexican paratype of X. monstrosa is shown initially followed by the holotype of X. churro and then the collection of both specimens.
  3. Video 3: Sediment near a hydrothermal vent at ~3,700 metres in the Pescadero Basin, Gulf of California, Mexico. (17.29 MB, Download)
    ROV Doc Ricketts dive 757, April 24, 2015. The video shows the female paratype of X. profunda gliding over the sediment in an S-pattern amongst polynoid scaleworms, sea anemones and vesicomyid clams. The video is speeded up to x6 times.

Zip files

  1. Supplementary Information (310 KB)

    This zipped file contains Supplementary Tables 1-5 and a Supplementary Table guide.

Additional data