Michael Raupach - Invertebrates Plenary

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Biodiversity assessment of the North Sea fauna using DNA barcodes and oher molecular methods

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Michael Raupach - Invertebrates Plenary

  1. 1. Analysing the marine fauna of the North Sea:A molecular approach using various methods Michael J. Raupach
  2. 2. Hotspots of species diversity © Julian Gutt/AWI © Wikipedia © Robin Moore
  3. 3. Hotspot of species diversity? © Nordsee von obenNorth Sea © Nordsee von oben © Nordsee von oben © Nordsee von oben © Wikipedia © Nordsee von oben
  4. 4. © Wikipedia… not a stable sea …
  5. 5. Global map of cumulative human impact across 20 ocean ecosystem types Halpern et al. 2008
  6. 6. Routes, ports and centralities in the global cargo ship network Kaluza et al. (2010)
  7. 7. Invasive species World Ocean Review 2010
  8. 8. AG Molecular Taxonomy of Marine Organisms (est. summer 2010) Senckenberg am Meer / Germany Centre of Marine Biodiversity Research Dr. Michael J. Raupach Dr. Silke Laakmann Dr. Thomas Knebelsberger Dipl. Biol. Inga Mohrbeck Dipl. Biol. Thorben Hofmann Tech. Ass. Valeska Borges founded by Goal:Validation and development of molecular methods for the identification of the marine metazoan fauna of the North Sea
  9. 9. Concept: Barcoding of the North Sea Metazoa(COI, nuclear markers)
  10. 10. Echinodermata (19 species / 81 specimens) “Pisces” (32 / 187) Cnidaria (1 / 4) Chaetognatha (1 / 5) ”Polychaeta” (3 / 14) 0.01… in progress (BOLD) …• Bryozoa• Pantopoda ”Crustacea”• Mollusca (81 / 502)• Porifera (Sponge BoL)• Ascidia• Aves• Mammalia•…
  11. 11. Combining data: • Aves • “Crustacea” • Insecta • Mollusca • “Pisces“
  12. 12. Two case studies: Crustacea FishSession Marine (C20) Session Fish 1 (B41)
  13. 13. Potential pitfalls using CO1 … • introgressive hybridization/incomplete lineage sorting • co-amplification of numts • heteroplasmy• presence of inherited endosymbionts (e.g. Wolbachia or Rickettsia) > linkage disequilibrium with mtDNA • no barcoding gap
  14. 14. Supplementary nuclear markers: ribosomal expansion segments 18S rDNA: V7 18S rDNA: V4 Wuyts et al. 2001
  15. 15. Why using supplementary nuclear markers? One example ... 10 12 5 28 5 mm 26 10 31 8 © Wikipedia Ligia oceanica (Linne, 1767)
  16. 16. • K2P: 0 - 5.4% • split is also supported by 16S rDNA 25 additional mutation steps!MP Network (TCS): COI
  17. 17. 18S rDNA: V4, V7 > no variation (0%)> evidence for gene flow on nuclear level > not two but only one species (also supported by morphometric and morphological studies)
  18. 18. Barcoding Analysis of of the North Sea environmental Metazoa samples(COI, nuclear markers)
  19. 19. Analysis of environmental samples Case study: Zooplankton Silke Laakmann and Inga MohrbeckZooplankton > heterogeneous mix of different organisms, including both small protozoans and large metazoans of different life stages with a size between 80 – 500 µm www.tafi.org.au/zooplankton/index.html
  20. 20. Idea / Plans:1. Inventory of species > buildup of a sequence library (COI, 18S rDNA) Session Marine (C19)
  21. 21. Idea / Plans:1. Inventory of species > buildup of a sequence library (COI, 18S rDNA) 2. Seasonal survey of zooplankton communities to document shifts in species composition using next-generation sequencing methods
  22. 22. Used markers:18S rDNA: V1 + V2 Wuyts et al. 2001
  23. 23. Barcoding Analysis of of the North Sea environmental Metazoa samples(COI, nuclear markers) Design of rapid tests for specific species identification
  24. 24. Design of molecular test systems for specific species identification Case study: commercial fish Thomas Knebelsberger and Torben Hofmann Thomas Knebelsberger The next step: rapid molecular in situ species identification Parallel Talk, Marine Barcoding, Napier 210, Friday, 14:15 to 14:30 Join it! I will …
  25. 25. Most important player Specific species identification
  26. 26. DNA- and Tissue Bank Barcoding Analysis of of the North Sea environmental Metazoa samples(COI, nuclear markers) Design of rapid tests for specific species identification Long-term storage of specimens and samples
  27. 27. Many different taxa – many different ways of handling
  28. 28. Work flow part I: specimen data acquisition “Trust on proven, tested and simple systems” sample Fixation (DESS, ethanol 96%) identification by experts specimen Specimen information • running number (unique code) • specimen details • sample information • taxonomic lineage (WoRMS) • collection data • photography • DNA datamodified BOLD excel sheets
  29. 29. Work flow part II: molecular data acquisition data base MOTU sequencesvoucher collection and sequence data base sequencing extraction DNA tissue sample specimen DNA extract work aliquot (freezer) tissue bank DNA bank (QiaSafe)
  30. 30. Thanks to …Wilko Ahlrichs • Rudi Amann • Jan Beermann • Olaf Bininda-Emonds •Maarten Boersma • Luisa Borges • Dirk Brandis • Gary Carvalho • FilipeCosta • Simon Creer • Nicole Dubilier • Christiane Eichner • Günther Fuchs •Frank-Oliver Glöckner • Paul Hebert • Sabine Holst • Jonas Keiler •Alexander Kieneke • Matthias Kloppmann • Florian Leese • Peter Lienau •Alexandra Markert • Pedro Martinez-Arbizu • Ole Stan Møller • HermannNeumann • Thurid Otto • Stefan Richter • Ursula Siebert • ChristophSchubart • Sabine Schückel • Ulrike Schückel • Myriam Schüller • MartinSchulze-Dieckhoff • Dirk Steinke • Sven Thatje • Hilde van Pelt • AchimWehrmann • …
  31. 31. END

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