IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0050437.html
   My bibliography  Save this article

Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes

Author

Listed:
  • Malcolm S Hill
  • April L Hill
  • Jose Lopez
  • Kevin J Peterson
  • Shirley Pomponi
  • Maria C Diaz
  • Robert W Thacker
  • Maja Adamska
  • Nicole Boury-Esnault
  • Paco Cárdenas
  • Andia Chaves-Fonnegra
  • Elizabeth Danka
  • Bre-Onna De Laine
  • Dawn Formica
  • Eduardo Hajdu
  • Gisele Lobo-Hajdu
  • Sarah Klontz
  • Christine C Morrow
  • Jignasa Patel
  • Bernard Picton
  • Davide Pisani
  • Deborah Pohlmann
  • Niamh E Redmond
  • John Reed
  • Stacy Richey
  • Ana Riesgo
  • Ewelina Rubin
  • Zach Russell
  • Klaus Rützler
  • Erik A Sperling
  • Michael di Stefano
  • James E Tarver
  • Allen G Collins

Abstract

Background: Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings: We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance: These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.

Suggested Citation

  • Malcolm S Hill & April L Hill & Jose Lopez & Kevin J Peterson & Shirley Pomponi & Maria C Diaz & Robert W Thacker & Maja Adamska & Nicole Boury-Esnault & Paco Cárdenas & Andia Chaves-Fonnegra & Elizab, 2013. "Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes," PLOS ONE, Public Library of Science, vol. 8(1), pages 1-16, January.
  • Handle: RePEc:plo:pone00:0050437
    DOI: 10.1371/journal.pone.0050437
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050437
    Download Restriction: no

    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0050437&type=printable
    Download Restriction: no

    File URL: https://libkey.io/10.1371/journal.pone.0050437?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Gordon D. Love & Emmanuelle Grosjean & Charlotte Stalvies & David A. Fike & John P. Grotzinger & Alexander S. Bradley & Amy E. Kelly & Maya Bhatia & William Meredith & Colin E. Snape & Samuel A. Bowri, 2009. "Fossil steroids record the appearance of Demospongiae during the Cryogenian period," Nature, Nature, vol. 457(7230), pages 718-721, February.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Malory O. Brown & Babatunde O. Olagunju & José-Luis Giner & Paula V. Welander, 2023. "Sterol methyltransferases in uncultured bacteria complicate eukaryotic biomarker interpretations," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Kang, Shijie & Zhang, Shijing & Wang, Zhendong & Li, Shengli & Zhao, Fangci & Yang, Jie & Zhou, Lingbo & Deng, Yang & Sun, Guidong & Yu, Hongdong, 2023. "Highly efficient catalytic pyrolysis of oil shale by CaCl2 in subcritical water," Energy, Elsevier, vol. 274(C).
    3. Jikun Liu & Litao Wang & Fei Chen & Wenya Hu & Chenglong Dong & Yinghao Wang & Yehua Han, 2023. "Molecular Characterization of Hydrocarbons in Petroleum by Ultrahigh-Resolution Mass Spectrometry," Energies, MDPI, vol. 16(11), pages 1-16, May.
    4. Lennart Ramme & Tatiana Ilyina & Jochem Marotzke, 2024. "Moderate greenhouse climate and rapid carbonate formation after Marinoan snowball Earth," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    5. Katsuhiko Shimizu & Michika Nishi & Yuto Sakate & Haruka Kawanami & Tomohiro Bito & Jiro Arima & Laia Leria & Manuel Maldonado, 2024. "Silica-associated proteins from hexactinellid sponges support an alternative evolutionary scenario for biomineralization in Porifera," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    6. T. Brunoir & C. Mulligan & A. Sistiaga & K. M. Vuu & P. M. Shih & S. S. O’Reilly & R. E. Summons & D. A. Gold, 2023. "Common origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    7. Huyue Song & Zhihui An & Qin Ye & Eva E. Stüeken & Jing Li & Jun Hu & Thomas J. Algeo & Li Tian & Daoliang Chu & Haijun Song & Shuhai Xiao & Jinnan Tong, 2023. "Mid-latitudinal habitable environment for marine eukaryotes during the waning stage of the Marinoan snowball glaciation," Nature Communications, Nature, vol. 14(1), pages 1-9, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0050437. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.