Skip to main content Skip to main navigation menu Skip to site footer
Correspondence
Published: 2022-10-12

Keratose sponge MuseOMICS: setting reference points in dictyoceratid demosponge phylogeny

Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Potsdam, Germany,
Queensland Museum, Biodiversity & Geosciences Program, P.O. Box 3300, South Brisbane, Queensland, Australia 4101. Griffith Institute for Drug Discovery, Griffith University, Brisbane 4111, Queensland, Australia 4School of Biological Sciences, University of Queensland, St Lucia, Queensland, 4072 Australia
Department of Earth- and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Potsdam, Germany,
Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences, University of Potsdam, Potsdam, Germany,
University Museum, Department of Natural History, University of Bergen, Bergen, Norway
Department of Earth- and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität, Munich, Germany. GeoBio-Center, Ludwig-Maximilians-Universität, Munich. Bavarian State Collection of Palaeontology and Geology, Munich, Germany
5Department of Earth- and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität, Munich, Germany. GeoBio-Center, Ludwig-Maximilians-Universität, Munich
Porifera

References

  1. Agne, S., Straube, N., Preick, M. & Hofreiter, M. (2022). Simultaneous barcode sequencing of diverse museum collection specimens using a mixed RNA bait set. Frontiers in Ecology and Evolution. https://doi.org/10.3389/fevo.2022.909846
    Burton, M. (1934) Scientific Reports: Great Barrier Reef Expedition 1928-29. Sponges.
    Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution, 17, 540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
    Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L. & Meyer, M. (2013) Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proceedings of the National Academy of Sciences of the United States of America, 110, 15758–15763. https://doi.org/10.1073/pnas.1314445110
    de Cook, S.C. & Bergquist, P.R. (2002a) Family Spongiidae Gray, 1867. In: J.N.A. Hooper and R.W.M. Van Soest (Eds.), Systema Porifera. A guide to the classification of sponges. Kluwer Academic/ Plenum Publishers, New York, Boston, Dordrecht, London, Moscow, pp. 1051–1060. https://doi.org/10.1007/978-1-4615-0747-5
    de Cook, S.C. & Bergquist, P.R. (2002b) Family Thorectidae Bergquist, 1978. In: J. N. A. Hooper and R. W.M. Van Soest (Eds.), Systema Porifera. A guide to the classification of sponges. Kluwer Academic/ Plenum Publishers, New York, Boston, Dordrecht, London, Moscow, pp. 1028–1050. https://doi.org/10.1007/978-1-4615-0747-5
    Erpenbeck, D., Ekins, M., Enghuber, N., Hooper, J.N.A., Lehnert, H., Poliseno, A., Schuster, A., Setiawan, E., De Voogd, N.J., Wörheide, G. & Van Soest, R.W.M. (2016) Nothing in (sponge) biology makes sense – except when based on holotypes. Journal of the Marine Biological Association of the United Kingdom, 96, 305–311. https://doi.org/10.1017/S0025315415000521
    Erpenbeck, D., Galitz, A., Ekins, M., Cook, S. de C., van Soest, R.W.M., Hooper, J.N.A. & Wörheide, G. (2020) Soft sponges with tricky tree: On the phylogeny of dictyoceratid sponges. Journal of zoological systematics and evolutionary research = Zeitschrift für zoologische Systematik und Evolutionsforschung, 58, 27–40. https://doi.org/10.1111/jzs.12351
    Erpenbeck, D., Sutcliffe, P., Cook, S. de C., Dietzel, A., Maldonado, M., van Soest, R.W.M., Hooper, J.N.A. & Wörheide, G. (2012) Horny sponges and their affairs: On the phylogenetic relationships of keratose sponges. Molecular Phylogenetics and Evolution, 63, 809–816. https://doi.org/10.1016/j.ympev.2012.02.024
    Gansauge, M.-T., Gerber, T., Glocke, I., Korlevic, P., Lippik, L., Nagel, S., Riehl, L.M., Schmidt, A. & Meyer, M. (2017) Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Research, 45, e79. https://doi.org/10.1093/nar/gkx033
    Hofreiter, M., Jaenicke, V., Serre, D., von Haeseler, A. & Pääbo, S. (2001) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research, 29, 4793–4799. https://doi.org/10.1093/nar/29.23.4793
    Hooper, J.N.A. & Wiedenmayer, F. (1994) Porifera. In: A. Wells (Ed), Zoological Catalogue of Australia. CSIRO, Melbourne, pp. 1–621 [Revised online version 2004 www.environment.gov.au/biodiversity/abrs/online–resources/fauna/afd/taxa/porifera/]. https://doi.org/10.1093/bioinformatics/btr509
    Huang, J.M., Yuan, H. & Li, C.H. (2021) Protocol for Cross-species Target-gene Enrichment. Bio-protocol, e1010606. https://doi.org/10.21769/BioProtoc.1010606
    Katoh, K. & Standley, D.M. (2013) MAFFT Multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780. https://doi.org/10.1093/molbev/mst010
    Li, H. (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27, 2987–2993. https://doi.org/10.1093/bioinformatics/btr509
    Li, H. & Durbin, R. (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25, 1754–1760. https://doi.org/10.1093/bioinformatics/btp324
    Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17, 10–12. https://doi.org/10.14806/ej.17.1.200
    Paijmans, J.L.A., Baleka, S., Henneberger, K., Taron, U., Trinks, A., Westbury, M. & Barlow, A. (2017) Sequencing single-stranded libraries on the Illumina NextSeq 500 platform. arXiv [Preprint] https://doi.org/10.48550/arXiv.1711.11004
    Rohland, N., Siedel, H. & Hofreiter, M. (2004) Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens. BioTechniques, 36, 814–6, 818–21. https://doi.org/10.2144/04365ST05
    Straube, N., Lyra, M.L., Paijmans, J.L.A., Preick, M., Basler, N., Penner, J., Rödel, M.-O., Westbury, M.V., Haddad, C.F.B., Barlow, A. & Hofreiter, M. (2021) Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Molecular Ecology Resources, 21, 2299–2315. https://doi.org/10.1111/1755-0998.13433
    Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A. & Minh, B.Q. (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44, W232–5. https://doi.org/10.1093/nar/gkw256

  2.