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Matthias Obst


Researcher and Project leader

Department of Biological and Environmental Sciences,
Systematics and Biodiversity
Göteborg University
Box 463
SE-405 30 Göteborg

Tel: 46 (0) 31-786 36 62
Fax: 46 (0) 31-41 67 29

Email: matthias.obst@bioenv.gu.se

Matthias Obst is a member of the The Linnaeus Centre for Marine Evolutionary Biology www.cemeb.science.gu.se


BioVeL: Biodiversity Virtual e-Laboratory (BioVeL homepage)
Biodiversity Virtual e-Laboratory (BioVeL) is an interdisciplinary project which will develop tools for pipelining data and analysis into efficient workflows, urgently needed to understand biodiversity in a rapidly changing environment. BioVeL customises, deploys and supports the Taverna/ myExperiment / BioCatalogue family of software to achieve this. Using agile processes, BioVeL defines and deploys (web) service sets and workflow packs catering for subcommunities within the a selected number of important areas of biodiversity science. These are: i) DNA sequence-based phylogeny and metagenomics services that provide a measure of genetic diversity used in conservation planning and that help to understand adaptation in relation to climate change; ii) Taxonomy services to provide the underpinning checklist of diversity in Europe, identification aids to native, invasive and economic species; iii) Niche and population modeling for species, to better understand the processes of conservation and invasive species management; and, iv) Ecosystem functionality and valuation services, to improve modeling capabilities to ecosystem services and CO2 sequestration.

LifeWatch (LifeWatch homepage)
Marine ecosystems provide a wide range of economically important products and services to the community and these functions are directly dependent on the biological diversity in these environments. Today, we note major changes in the biodiversity composition of our marine ecosystems, but we have poor control over how large and extensive they are because there is no organized and standardized monitoring system over a wider geographical perspective. At the same time there is no analytical approach available that combines diverse biological disciplines, i.e. ecological, taxonomic, climatic, and genetic data. The practical impossibility to assemble and analyze such complex data sets across large geographic distances is perhaps the most crucial obstacle for biodiversity research to become a dominant scientific discipline in the future. A part of my research will focuses on facilitating meta-analysis of such diverse information in order to understand the changes and functions in marine ecosystems.

Swedish LifeWatch (http://www.slu.se/lifewatch)
A consortium of the important providers and users of biodiversity data at Swedish universities, natural history museums and governmental agencies, will develop a National Infrastructure for Biodiversity Data, based on common standards, distributed databases, web services, and a focal LifeWatch Analysis Platform. At this Platform, all biodiversity data, as well as environmental explanatory variables, will be accessible without transformations and possible to explore and analyse with R statistics, tools for spatial and temporal analyses, and modelling tools for prediction. Here, the researcher can also upload own data and maps and take advantage of the tools as well as data from other sources. Furthermore, we will develop an interface to the next generation of the Species Gateway (Artportalen.se), enabling researchers to adapt the Gateway to suite the researchers’ own demands, e.g. by adding an unlimited number of own variables and decide when to make the data accessible for others. The Swedish LifeWatch Analyses Portal will give opportunities to explore issues never reachable before, e.g. by easily combining data from several primary databases, life history parameters (enabling specific selections), with environmental data, applied to advanced analytical tools.

EMBOS - Development and implementation of a pan-European Marine Biodiversity Observatory System (EMBOS homepage)
Marine biodiversity varies over large scales of time and space, and requires a research strategy beyond the tradition/capabilities of classic research. Research that covers these scales requires a permanent international pan-European network of observation stations with an optimized and standardized methodology. In EMBOS the needed large-scale network of research locations in Europe will be installed to assess long-term changes in marine biodiversity and their possible causes taking into account natural and anthropogenic gradients, and EMBOS will extend and optimize this observatory system, including novel interdisciplinary approaches for research. The cooperation leads to a focused and cost effective long term research agenda for EU marine observatories, and contributes to ERA, LIFEWATCH and GEOSS/GEOBON actions, and supports legal obligations of the EU regarding the CBD, OSPAR and Barcelona conventions as well as EU directives (Bird and Habitat Directive, WFD,MSFD, ICZM).

Genomics Observatories Network (homepage). The Genomic observatory Network initiative will build a global network of premier research sites working to generate genomic observations that are well contextualized and compliant with global data standards. To coordinate a set of long-term, place-based, DNA-centric programs that quantify biotic interactions in an ecosystem and develop models of biodiversity to predict the quality and distribution of ecosystem services. I am currently working on the integration of genomic indicators in marine monitoring programs and Marine Biodiversity Observatory Networks.

Important links

BioVeL – Biodiversity Virtual Laboratory (http://biovel.eu/)
LifeWatch (http://www.lifewatch.eu/)
Swedish LifeWatch (http://www.slu.se/lifewatch)
EMBOS - Development and implementation of a pan-European Marine Biodiversity Observatory System
MG4U - Marine Genomics for Users (http://www.mg4u.eu/)

Matthias Obst – Publication record 2003-2013

Peer-reviewed articles:

1. Gärdenfors U, Jönsson M, Obst M, Wremp AM, Kindvall O, Nilsson J (2014) Swedish LifeWatch ─ a biodiversity infrastructure integrating and reusing data from citizen science, monitoring and research. Human Computation 1(2): 147-161.

2. Mathew C, Guentsch A, Obst M, Vicario S, Haines R, Williams AR, de Jong Y, Goble C (2014) A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control Biodiversity Data Journal 2: e4221. DOI: 10.3897/BDJ.2.e4221.

3. Davies N, Field D, Amaral-Zettler L, Clark M, Deck J, Drummond A, Faith D, Geller J, Gilbert J, Gloeckner FO, Hirsch P, Leong JA, Meyer C, Obst M, Planes S, Scholin C, Vogler A, et al. (2014) The Founding Charter of the Genomic Observatories Network. Giga Science 3: 2.

4. Bourlat SJ, Borja A, Gilbert J, Taylor MI, Davies N, Weisberg SB, Griffith JF, Lettieri T, Field D, Benzie J, Glöckner FO, Rodríguez-Ezpeleta N, Faith DP, Bean TP, Obst M (2013) Genomics in marine monitoring: New opportunities for assessing marine health status. Marine Pollution Bulletin 74(1): 19–31. http://www.sciencedirect.com/science/article/pii/S0025326X1300289

5. Nakano H, Lundin K, Bourlat SJ, Telford MJ, Funch P, Obst M, Thorndyke MC (2013) Xenoturbella bocki has direct development with similarities to Acoelomorpha, Nature Communications 4:1537, DOI: 10.1038/ncomms2556

6. Moosbrugger M, Schwaha T, Walzl MG, Obst M, Ostrovsky AN (2012) The placental analogue and the pattern of sexual reproduction in thecheilostome bryozoan Bicellariella ciliata (Gymnolaemata). Frontiers in Zoology 9(29).

7. Obst M, Faurby S, Bussarawit S, Funch P (2012) Molecular phylogeny of extant horseshoe crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species. Molecular Phylogenetics and Evolution 62(1): 21-26.

8. Sköld HN and Obst M (2011) Potential for clonal animals in longevity and ageing studies. Biogerontology 12 (5). 387-396.

9. Obst M, Nakano N, Bourlat SJ, Thorndike M, Telford M, Nyengaard JR, Funch P (2011) The spermatozoan ultrastructure of Xenotubella bocki Westblad 1949. Acta Zoologica. 92(2): 109-115.

10. Faurby S, King TL, Obst M, Pertoldi C, Funch P (2010) Population dynamics of American horseshoe crabs – a story of historic climatic events and recent anthropogenic pressures. Molecular Ecology 19 (15): 3088-3100.

11. Fuchs J, Iseto T, Hirose M, Sundberg P, Obst M (2010) The first internal molecular phylogeny of the phylum Entoprocta (Kamptozoa). Molecular Phylogenetics and Evolution 56 (1): 370-379.

12. Schander C, Rapp HT, Kongsrud JA, Bakken T, Berge J, Cochrane S, Oug E, Byrkjedal I, Todt C, Cedhagen T, Fosshagen A, Gebruk A, Larsen K, Levin L, Obst M, Pleijel F, Stöhr S, Warén A, Mikkelsen NT, Hadler-Jacobsen S, Keuning R, Petersen KH, Thorseth IH, Pedersen RB (2010) The fauna of hydrothermal vents on the MohnRidge (North Atlantic). Marine Biology Research 6:155-171.

13. Kjeldsen KU, Obst M, Nakano H, Funch P, Schramm A (2010) Two types of endosymbiotic bacteria in the enigmatic marine worm Xenoturbella. Applied and Environmental Microbiology 76(8): 2657–2662.

14. Hejnol A, Obst M, Stamatakis A, Ott M, Rouse GW, Edgecombe GD, Martinez P, Baguñà J, Bailly X, Jondelius U, Wiens M, Müller WEG, Seaver E, Wheeler WC, Martindale MQ, Giribet G, Dunn CW (2009) Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedingsof the Royal Society B 276, 4261–4270.

15. Fuchs J, Obst M, Sundberg P (2009) The first comprehensive molecular phylogeny of Bryozoa (Ectoprocta) based on combined analysis of nuclear and mitochondrial genes. Molecular Phylogenetics and Evolution 52: 225-233.

16. Funch P, Thor P, Obst M (2008) Symbiotic relations and feeding biology of Symbion pandora (Cycliophora) and Triticella flava (Bryozoa). Life and Environment 58(2): 185-188.

17. Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G (2008) Broad phylogenomic sampling improves resolution of the Animal Tree of Life. Nature 452 (7188): 745-750.

18. Bourlat SJ, Nakano H, Åkerman M, Telford MJ, Thorndyke MC, Obst M (2008) Feeding ecology of Xenoturbella bocki (phylum Xenoturbellida) revealed by genetic barcoding. Molecular Ecology Resources 8: 18-22.

19. Obst M and Funch P. (2006) The microhabitat of Symbion pandora (Cycliophora) on the mouthparts of its host Nephrops norvegicus (Decapoda: Nephropidae). Marine Biology 148 (5): 945-951.

20. Obst M, Funch P, Kristensen RM (2006) A new species of Cycliophora from the mouthparts of the American lobster Homarus americanus (Nephropidae, Decapoda). Organisms, Diversity & Evolution 6: 83-97.

21. Obst M, Funch P, Giribet G (2005) Hidden diversity and host specificity in cycliophorans; a phylogeographic analysis along the North Atlantic and Mediterranean Sea. Molecular Ecology 14 (14) 4427-4440.

22. Riisgaard HU, Kollerup Nielsen K, Fuchs J, Fønss Rasmussen B, Obst M, Funch P. (2004) Ciliary feeding structures and particle capture mechanism in the freshwater bryozoan Plumatella repens (Phylactolaemata). Invertebrate Biology 123:156-167.

23. Obst M and Funch P. (2003) Dwarf male of Symbion pandora (Cycliophora). Journal of Morphology 255: 261-278.


1. Stelzer K, Heyer K, Bourlat SJ, Obst M (2013) Application of Niche Modeling and Earth Observation for the risk assessment and monitoring of invasive species in the Baltic Sea. Report to the European Space Agency. Available for download here https://www.dropbox.com/sh/u4ut7ykdmrzb0xz/WKUAITchzS

Peer-reviewed book chapters, review articles, and conference contributions:

1. González-Talaván A, Mathew C, Obst M, Paymal E (2014). Data Refinement Using the BioVeL Portal. 67 pp. Copenhagen: Global Biodiversity Information Facility. Available online at http://www.gbif.org/orc/?doc_id=5983.

2. Holl S., Garijo D, Belhajjam K, Zimmermann O, Giovanni RD, Obst M, Goble C (2013) On specifying and sharing scientific workflow optimization results using research objects. Proceedings of the 8th Workshop on Workflows in Support of Large-Scale Science. Denver, Colorado 28-37, 2013. DOI 10.1145/2534248.2534251

3. Davies N, Field D, Amaral-Zettler L, Barker K, Bicak M, Bourlat S.J., Coddington J, Deck J, Drummond A, Gilbert J, Glöckner FO, Kottmann R, Meyer C, Morrison N, Obst M, et al. (2014) Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012. Standards in Genomic Science. Standards in Genomic Science 9 (3): 1236-1250, doi:10.4056/sigs.4319681.

4. Hardisty et al., (2013) A decadal view of biodiversity informatics: challenges and priorities. BMC Ecology: 13:16, doi:10.1186/1472-6785-13-16.

5. Giribet G, Dunn CW, Edgecombe G, Hejnol A, Kristensen RM, Martindale MQ, Obst M, Rouse G, Seaver E, , Sørensen MV, Wheeler WC, Worsaae K(2010) Reconstructing the Protostome Tree of Life – The past, the present, and the future. Cladistics 26(2): 211-211.

6. Sköld HN, Obst M, Sköld M, Åkesson B (2009) Stem cells in asexual reproduction of marine invertebrates, Chapter 5. In: Matranga V & Rinkevich B (eds.) Stem Cells in Marine Organisms, pp. 105-138.

7. Dunn CW, Hejnol A,Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SHD, Schmidt-Rhaesa A, Okusu A, Kristensen RM, Wheeler WC, Martindale MQ, Giribet G (2008) New Insight into Animal Relationships from Phylogenomic Analyses. Journal of Morphology 269: 1464-1464.

8. Nakano H, Bourlat SJ, Obst M, Nakano A, Telford M, Thorndyke M (2008) Developmental Studies of Xenoturbella. Journal of Morphology 269: 1477-1478.

9. Obst M, Nakano H, Bourlat SJ, Thorndike MC, Telford MJ, Nyengaard JR, Funch P (2008) The spermatozoan ultrastructure of Xenotubella suggests a close relationship to enteropneust hemichordates. Journal of Morphology 269: 1478-1478.

10. Fuchs J, Obst M, Sundberg P (2008) The Bryozoa of Sweden - Morphological and Molecular Data in Modern Taxonomic Research. Journal of Morphology 269: 1485-1485.

11. Dupont S, Obst M, Wilson K, Sköld H, Nakano H, and Thorndyke M (2007) Marine Ecological Genomics - When Genomics meets Marine Ecology. Marine Ecology Progress Series 332: 257–273.

12. Funch P, Sørensen MV, Obst M. (2005) On the phylogenetic position of Rotifera - have we come any further? Hydrobiologia 546: 11-28.

13. Obst M (2003) Cycliophoran relationships revisited. Cladistics 19: 159-160.

Popular science articles/presentations:

1. Lundin K, Obst M (2013) Paradoxmasken håller ställningen som vår anfader. Fauna & Flora 108(1): 42-43

2. Sundin R, Obst M (2009) Rik svenskt mossdjurfauna. Fauna & Flora 104 (4): 54

3. Obst M (2009) Grzimek's animal life encyclopedia: Bryozoa

4. Obst M (2008) Auf den Spuren von Linné. Unity 1:12-13.

5. Funch P, Obst M, Wang T (2008) Dolkhalers fysiologi, genetiske diversitet og udbredelse. In: Jörgensen L (ed.) Galathea 3, pp. 222-227.

6. Obst M, Dupont S, Thorndyke M. (2007) In the footsteps of Linnaeus - Microscopic Imaging in Marine Biodiversity Research. Resolution – Leica Research Newsletter 2: 3-6.

7. Obst M and Fuchs J (2007) Skönhet under luppen. Fauna och Flora 102 (4): 16-22.

8. Obst M (2004) Rinbærernes diversitet og evolution. Danske Naturhistorisk Forening Årskrift nr. 14 - 2003/2004: 60-63

Recent press releases and radio features:

1. Genomic Observatories, Interview http://www.youtube.com/watch?v=7Lu-jD5apaI&list=PLgacjRIHqvMDTzhC1oMIoBZabUPzT8plj&index=10

2. Göteborgs universitet länk mellan BioVeL och LifeWatch

3. Biodiversity Virtual e-Laboratory launched

4. Samordnar forskningen om biologisk mångfald
http://www.science.gu.se/aktuellt/nyheter/Nyheter Detalj/samordnar-forskningen-om-biologisk-mangfald.cid1046642

5. Alla svenska arter samlas på nätet
http://www.science.gu.se/aktuellt/nyheter/Nyheter Detalj/alla-svenska-arter-samlas-pa-natet.cid945171

6. Klimatförändringar krymper bestånden av dolksvans
http://www.science.gu.se/aktuellt/nyheter/Nyheter Detalj/klimatforandringar-krymper-bestanden-av-dolksvans.cid954894

7. Lovén-centret ger namn åt ny art
http://www.science.gu.se/aktuellt/nyheter/Nyheter Detalj/lov-n-centret-ger-namn-at-ny-art-.cid930370

8. Vetenskapsradion. Radio feature: Vetenskapsnyheter, Sveriges Radio P1



Curriculum vitae - Matthias Obst

1. Doctoral degree
2004, PhD Biology, University of Aarhus (Denmark), subject area: Systematic biology, thesis title: Diversity and Evolution of Cycliophora, supervisor: Peter Funch

2. Postdoctoral work
2005-2008: Postdoctoral fellow of the Royal Swedish Academy, Kristineberg Marine Research Station, Sweden

4. Present position
2009-: Researcher in marine biology (50%) and project coordinator in EC-FP7 projects LifeWatch-BioVeL and Marine Genomics for Users (50%) at the Department of Zoology, Göteborg University, Sweden

5. Paternal leave
October 2009 – February 2010 (5 months); April – August 2011 (5 months)

6. Supervision of phd students
Judith Fuchs, disputation March 2011, Department of Zoology, University of Gothenburg, Sweden

7. Personal data
Birth place/date, 18. Aug 1974 in Erfurt (Germany); citizenship (German); maritalstatus (engaged, father of two children, both have Swedish citizenship)

8. Languages
German (native), English, Danish, Swedish

9. Areas of expertise
Invertebrate phylogeny and systematics, marine phylogeography, molecular taxonomy, barcoding, phylogenomics, metagenomics, e-science, complex life cycles, zoomorphology, meiofauna, marine and benthic ecology, marine conservation biology

10. Scientific publications
Author/coauthor of 41 publications in English, Danish, German, and Swedish (incl. peer-reviewed papers in scientific journals and books, publications in cited conference proceedings, and popular scientific articles). Overall number of Scopus citations 998. h-index = 10.

11. Current projects and grants >100 kSEK (since 2010)
2013-2015: Species identification pipelines for analyzing marine invertebrate larval stages, community structure, and trophic interactions (Biodiversity genomics), Swedish Research Council funded, link
2011-2014: Biodiversty Virtual e-Laboratory (BIOVEL), FP7 funded, http://www.biovel.eu
2011-2015: Development of a pan-European Marine Biodiversity Observatory System (EMBOS), VINNOVA/COST funded, http://www.embos.eu
2010-2014: Swedish LifeWatch (SLW), Swedish Research Council funded, http://www.slu.se/lifewatch
2010-2013: Marine genomics for Users (MG4U), FP7 funded, http://www.mg4u.eu

12. Member of professional bodies (function)
Group on Earth Observation GEO (task leader for Global Ecosystem Monitoring), Genomics observatories network (steering board member), Swedish LifeWatch consortium (chairman), Nordic LifeWatch consortium (Management committee member), Genomics Standards Consortium (member), ppLifeWatch Europe (Policy & Science Board member, Management Committeemember), Marine Genomics 4 Users (Management committee member), EMBOS (Management committee member), Marine Genomics Network of Excellence (team leader), Tree of Life Consortium (member)

13. Methods
Sampling methods: diving, epi-/benthic sampling, plankton sampling
Analytical methods: Light- and fluorescence microscopy, Confocal laser scanning microscopy, Transmission- and scanning electron microscopy, FISH, PCR-based and high-throughput sequencing, EST/Genomic analysis, TAVERNA based workflows

14. Marine expeditions
2009: Bioskag II expedition (Inventory of the marine bottom fauna of the Norwegian Skagerrak); 2006-09: Pandalina expedition (Inventory of the marine bottom fauna of the Swedish west coast); 2007: Galathea3 expedition (conservation of Asian horseshoe crabs); 2006: Thailand (conservation of Asian horseshoe crabs); 1992-2004: East coast of USA, Woods Hole Laboratories 2003-2001: Kristineberg Marine Research Station, Sweden, 1998, 1996, 1994: Roscoff Marine Biological Station, France, 1995: Marine Biological Station Boinsdorf, Germany, 1992: Greenland

15. Vessel time and scientific cruises
2009 (2 weeks) Bottom dredging in Norway; 2008 (4 weeks) Bottom dredging in Skagerrak and Kattegat; 2007 (4 weeks) Bottom dredging in Skagerrak and Kattegat; 2007 (1 month) Deep water dredging and trawling in the North Atlantic; 2006 (4 weeks) Bottom dredging in Skagerrak and Kattegat

16. Supervision overall
Graduate students: JudithFuchs, Göteborg University, SE (Ph.D. 2011), Undergraduate students: Kasper K Nielsen, Aarhus University, DK (M.Sc. 2008), Judith Fuchs, Aarhus University, DK (M.Sc. 2004), Khy An, Aarhus University, DK (M.Sc. 2004)


Matthias Obst


Short movie about the BioVeL project

Interview about Genomic observatories

'Decoding the oceans'

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