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Saskia A. Otto

Postdoctoral Researcher

Work Experience


since 04/2014

Institute of Marine Ecosystem and Fisheries Science, University of Hamburg

Habilitation qualification position.


02/2012 - 03/2014

Stockholm Resilience Centre, Stockholm University

BEAM project: Size measurements and time series analysis; testing for patterns in size distribution, trends and thresholds in Baltic Sea pelagic food webs.


09/2010 - 11/2014

World Wide Fund (WWF)

Wild-fishery assessments and quality control for the annual seafood guide.

Research assistant and PhD student

04/2009 - 01/2012

Institute of Marine Ecosystem and Fisheries Science, University of Hamburg

AMBER project: Spatio-temporal analyses of zooplankton communities; testing for changes in productivity regimes and relative importance of trophic controls.


01/2008 - 02/2008

German Technical Cooperation (GTZ)

Aquaculture baseline study in the province Negros Occidental, Philippines; assessment of aquaculture farms (tilapia, milkfish, shrimps) for qualification of eco-label certification.

Research scientist

07/2007 - 03/2009

Institute of Inland Fisheries Potsdam-Sacrow

Development of server-based relational databases and ArcGIS geodatabase; fish and water quality monitoring (Water Framework and Habitat Directives).

Junior consultant

04/2007 - 05/2007

German Development Service (DED)

Training of local NGO, Philippines; study on heavy metal contamination in estuary and health impact assessment; coral reef monitoring and MPA establishment.


PhD in Biology (Dr. rer. nat.)


University of Hamburg, Department of Biology

Dissertation: Long-term population dynamics of key copepods under climate and food web changes: The Baltic Sea as a case study

Advisor: Christian Möllmann

Diploma (equivalent to M.Sc.) in Biology


Humboldt-University of Berlin, Department of Biology

Major: Zoology; Minors: Ecology, Geography

Thesis: The effects of temporal variability of disturbance on marine fouling communities at the GEOMAR, Kiel, and Leigh Marine Laboratory, University Auckland, NZ, within the framework of the international training and research program GAME

Key Skills


R, SQL, Matlab, HTML, CSS,
Git, Unix-Shell, Swift,


Supervised and unsupervised learning, spatio-temporal modelling, experimental design

Graphic Design

Adobe Photoshop & Illustrator, Affinity Designer, Procreate, RoughAnimator

Field & Lab

Onboard data collection,sampling and classification of pelagic and demersal fish, micro- and macroscopic analyses, digital image analysis (ZooScan), enzyme activity measurements, underwater coral reef measurements;
PADI rescue diver license (02/2008)




Co-chair of ICES WKINTRA

since 2018

(Workshop series on Integrated Trend Analysis)

Co-chair of ICES WGCERP

since 2019

(Working Group on Common Ecosystem Reference Points)


since 2016

(Working Group on Integrated Assessments of the Baltic)

Member since 2010

Member of ICES WGZE


(Working Group on Zooplankton Ecology)


Trainee Program (NFP)

04/2006 - 05/2007

German Development Service (DED)

International student training and research program (GAME)

10/2004 - 7/2005

Mercator Foundation

Funded Projects

Humboldt Tipping - Social-Ecological Tipping Points of the Northern Humboldt Current Upwelling System, Economic Repercussions and Governance Strategies

2019 - 2022

Funded by the DFG (German Research Foundation); co-leader of WP2 (work package on pressure-state relationships and fish production in the HUS)

RLab 2.0 - Modular environmental statistics: Script-based analyses with R for geography, meteorology or biology students

2018 - 2019

A research lab project funded by the University of Hamburg

BLUEWEBS - Blue growth boundaries in novel Baltic food webs

2017 - 2020

BONUS ERA-NET funded project

MARmaED - MARine MAnagement and Ecosystem Dynamics under climate change

2015 - 2019

EU-funded Innovative Training Network program

FUNBAZOO - FUNctional diversity of BAltic ZOOplankton

2015 - 2017

Funded by the federal state Hamburg; project coordinator

IEA-Exchange - Exchange of knowledge for Integrated Ecosystem Assessment

2015 - 2016

ICES Science Fund; project coordinator

Ecosystem-based approach for developing and testing pelagic food web indicators

2014 - 2016

funded by the Swedish Environmental Protection Agency (SEPA) and Swedish Agency for Marine and Water Management (see Swedish summary); project coordinator

BEAM – Baltic Ecosystem Adaptive Management

2010 - 2015

Stockholm University program; postdoc

AMBER - Assessment and Modeling of Baltic Ecosystem Response

2009 - 2011

BONUS ERA-NET funded project; PhD


INDperform logo


R package for evaluating ecological state indicators and assessing the ecological status based on a suite of indicators.


University of Hamburg


  • MARSYS-4: Introduction to computer programming in R, data exploration and visualization, and statistical modelling (master level; 6 semesters) - see online course at MARinE Data Science github repo
  • MARSYS-11: Introduction to inferential statistics and experimental design, Generalized Linear and Additive Models, multivariate stats (master level; 5 semesters)
  • BMARSYS-6: Introduction to computer programming in R, data exploration and visualization (bachelor level; 1 semester) - see German online course at MARinE Data Science github repo
  • BMARSYS-12: Multivariate statistics with R (bachelor level; 1 semester)

Teaching Assistant

  • MARSYS-10: Ecosystem management and environmental policy (master level; 6 semesters)
  • MARSYS-5: Field Methods in Biological Oceanography and Fishery Science (master level; semesters)
  • Basics in biostatistics (bachelor level; 3 semesters)

Stockholm University


  • Master Course 2: Systems theory and resilience thinking, module regime shifts (1 semester)
  • Invited instructor at a course on "Applied methods for research on regime shifts in socio-ecological systems" organized by The Beijer Institute of Ecological Economics, held in conjunction with the 5th World Congress of Environmental and Resource Economists in Istanbul, 27-29 June 2014


  • 3-day course on "Introduction to R" at the BSH (Federal Maritime and Hydrographic Agency of Germany), Hamburg, February 2019


Research Articles (peer-reviewed)

  • Beaugrand, G., Conversi, A., Atkinson, A., Cloern, J., Chiba, S., Fonda-Umani, S., Kirby, R.R., Greene, C.H., Goberville, E., Otto, S.A., Reid, P.C., Stemmann, L. & M. Edwards (2019): Prediction of unprecedented biological shifts in the global ocean. Nature Climate Change 9:237-243. DOI: 10.1038/s41558-019-0420-1
  • Kadin, M., Blenckner, T., Casini, M., Gårdmark, A., Torres, M. A. & S.A. Otto (2019): Trophic Interactions, Management Trade-Offs and Climate Change: The Need for Adaptive Thresholds to Operationalize Ecosystem Indicators. Frontiers in Marine Science 6:249. DOI: 10.3389/fmars.2019.00249
  • McQuatters-Gollop, A., Mitchell, I., Vina-Herbon, C., Bedford, J., Addison, P.F.E., Lynam, C.P., Geetha, P.N., Vermeulan, E.A., Smit, K., Bayley, D.T.I., Morris-Webb, E., Niner, H.J. & S.A. Otto (2019): From Science to Evidence – How Biodiversity Indicators Can Be Used for Effective Marine Conservation Policy and Management. Frontiers in Marine Science 6:109. DOI: 10.3389/fmars.2019.00109
  • Sguotti, C., Otto, S.A., Cormon, X., Werner, K.M., Deyle, E., Sugihara, G. & C. Möllmann (2019): Non-linearity in stock–recruitment relationships of Atlantic cod: insights from a multi-model approach. ICES Journal of Marine Science, fsz113. DOI: 10.1093/icesjms/fsz113
  • Sguotti, C., Otto, S.A., Frelat, R., Langbehn, T.J., Ryberg, M.P., Lindegren, M., Durant, J.M., Stenseth, N.C. & C. Möllmann (2019): Catastrophic dynamics limit Atlantic cod recovery. Proceedings of the Royal Society B-Biological Sciences, 286: 20182877. DOI: 10.1098/rspb.2018.2877
  • Frelat R., Orio A., Casini M., Lehmann A., Mérigot B., Otto S.A., Sguotti C. & C. Möllmann (2018): A three-dimensional view on biodiversity changes: spatial, temporal and functional perspectives on fish communities in the Baltic Sea. ICES Journal of Marine Science, 1-13. DOI: 10.1093/icesjms/fsy027
  • Otto, S.A., Kadin, M., Casini, M., Torres, M.A. & Blenckner, T. (2018): A quantitative framework for selecting and validating food web indicators. Ecological Indicators 84: 619-631. DOI: 10.1016/j.ecolind.2017.05.045.
  • Torres, M.A., Casini, M., Huss , M., Otto, S.A., Kadin, M. & A. Gårdmark (2017): Food-web indicators accounting for species interactions respond to multiple pressures. Ecological Indicators 77: 67–79. DOI: 10.1016/j.ecolind.2017.01.030
  • Klais, R., Otto, S.A., Teder, M., Simm, M. & H. Ojaveer (2017): Winter–spring climate effects on small-sized copepods in the coastal Baltic Sea. ICES Journal of Marine Science 74: 1855-1864. DOI: 10.1093/icesjms/fsx036
  • Frelat, R., Lindegren, M., Denker, T.S., Floeter, J., Fock, H.O., Sguotti, C., Stäbler M., Otto, S.A. & C. Möllmann (2017): Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities. PLoS One 12: e0188205. DOI: 10.1371/journal.pone.0188205
  • Dickey-Collas, M., McQuatters-Gollop, A., Bresnan, E., Kraberg, A.C., Manderson, J.P., Nash, R.D.M., Otto, S.A., Sell, A.F., Tweddle, J.F. & V.M. Trenkel (2017): Pelagic habitat: exploring the concept of good environmental status. ICES Journal of Marine Science 74: 2333–2341. DOI: 10.1093/icesjms/fsx158
  • Otto, S.A., Simons, S., Stoll, J.S. & P. Lawson (2016): Making progress on bycatch avoidance in the ocean salmon fishery using a transdisciplinary approach. ICES Journal of Marine Science 73: 2380–2394. DOI: 10.1093/icesjms/fsw061
  • Beaugrand, G., Conversi, A., Chiba, S., Edwards, M., Fonda-Umani, S., Greene, C., Mantua, N., Otto, S. A., Reid, P. C., Stachura, M. M., Stemmann, L. & H. Sugisaki (2015): Synchronous marine pelagic regime shifts in the Northern Hemisphere. Philosophical Transactions of the Royal Society B: Biological Sciences 370: 20130272. DOI: 10.1098/rstb.2013.0272
  • Downing, A.S., Hajdu, S., Hjerne, O., Otto, S.A., Blenckner, T., Larsson, U. & M. Winder (2014): Zooming in on size distribution patterns underlying species coexistence in Baltic Sea phytoplankton. Ecology Letters, 17, 1219-1227. DOI:
  • Otto, S.A., Llope, M., Kornilovs, G., & C. Möllmann (2014): Interactions among density, climate and food web effects determine long term dynamics of marine zooplankton species. Marine Ecology Progress Series, 498:73-84. DOI: 10.3354/meps10613
  • Otto, S.A., Diekmann, R., Flinkmann, J., Kornilovs, G. & C. Möllmann (2014): Habitat heterogeneity determines climate impact on zooplankton community structure and dynamics. PLoS ONE, 9(3): e90875. DOI: 10.1371/journal.pone.0090875
  • Tomczak, M.T., Heymans, J.J., Yletyinen, J., Niiranen, S., Otto, S.A. & T. Blenckner (2013): Ecological network indicators of ecosystem status and change in the Baltic Sea. PLoS ONE, 8(10): e75439. DOI: 10.1371/journal.pone.0075439
  • Lindegren, M., Dakos, V., Gröger, J.P., Gårdmark, A., Kornilovs, G., Otto, S.A. & C. Möllmann (2012): "Early detection of ecosystem regime shifts: a multiple method evaluation for management application. PLoS ONE, Vol 7(7): 1-9. DOI: 10.1371/journal.pone.0038410
  • Atalah, J., Otto, S.A., Anderson, M.J., Costello, M., Lenz, M. & M. Wahl (2007): "Temporal variance of disturbance did not affect diversity and structure of a marine fouling community in north-eastern New Zealand". Marine Biology, Vol. 153(2): 199-211. DOI: 10.1093/icesjms/fsy027

Book Chapter

  • Diekmann, R., Otto, S.A. & C. Möllmann (2012): Towards Integrated Ecosystem Assessments (IEAs) of the Baltic Sea - Investigating ecosystem state and historical development. In: "Climate Impacts on the Baltic Sea: From Science to Policy", Reckermann, M., Brander, K., MacKenzie, B.R., Omstedt A. (eds.), Springer Earth System Sciences Series, Berlin, Heidelberg, p. 161-201. ISBN 978-3-642-25728-5

Expert Reports

  • Kadin, M., Blenckner, T. & S.A. Otto (2018): Future pressures and management actions – Evaluation of proposed MSFD food-web indicators under different scenarios for the Baltic Sea. On behalf of the Swedish Agency for Marine and Water Management (Havs- och Vattenmyndigheten), 19 p.
  • Otto, S.A., Kadin, M., Torres, M.A., Casini, M., Huss, M., Blenckner, T. & A. Gårdmark (2017): Ecosystem-based approach for developing pelagic food-web indicators - final project report. Naturvårdsverket rapport 6788, ISBN 978-91-620-6788-5 (in Swedish)
  • Otto, S.A. & Zahn S. (2008): Assessment and development of an evaluation framework for fish and lamprey species in rivers and lakes within FFH protection areas in the state Brandenburg in 2007. On behalf of the Ministry of Rural Development, Environment and Agriculture of the Federal State of Brandenburg, 72 p. (in German)
  • Zahn, S., Otto, S.A. & Wolter, C. (2008): Fish assessment in selected rivers and lakes in the state Brandenburg - a baseline study for assessing the ecological status in the context of the European Water Framework Directive. On behalf of the Ministry of Rural Development, Environment and Agriculture of the Federal State of Brandenburg, 538 p. (in German)
  • Otto, S.A. & Zahn, S. (2008): Review on temperature and oxygen tolerances of anadromous fish species in the Elbe river. On behalf of the River Basin Community Elbe, 43 p. (in German)
  • Otto, S.A. & Zahn, S. (2007): B 183 OU Bad Liebenwerda - Expert report on the impact of a road construction project on protected fish and mussel species. On behalf of the road agency of the State of Brandenburg, 36 p. (in German)

Selected Presentations

(since 2015)

Integrated ecosystem assessments in ICES working groups

Invited speaker

Baltic Earth Workshop on 'Multiple drivers for Earth system changes in the Baltic Sea region', Tallin, Estonia

November 2018

Recent advances in indicator development and performance validation for ecosystem-based management

IMCC5 - International Marine Conservation Congress

June 2018

INDperform: an R package for validating ecological state indicator performances

ICES Annual Science Conference, Fort Lauderdale, U.S.A.

September 2017

On the lookout for suitable indicators for the Baltic pelagic food web - a potential evaluation framework


Lessons learned: Successes and pitfalls in IEA methods

ICES Annual Science Conference, Riga, Latvia

September 2016

Evaluating zooplankton indicators for the MSFD food-web descriptor under environmental gradients and non-linear interactions - is there a universal indicator?

ICES/PICES 6th Zooplankton Production Symposium

May 2016

Weak stock bycatch avoidance in the west coast ocean salmon fishery: a bioeconomic model using spatio-temporal data from commercial fishermen

American Fisheries Society Conference

August 2015

Other Media

General additive models and their application in modelling zooplankton lifecycle dynamics

Video presentation of seminar held during the BEAM PhD workshop "Modelling as a tool to study the Baltic Ecosystem"
March 2013, Askö laboratory; available at this Youtube link