PhD Courses in Denmark

Objectives of the course:

Ecological connectivity can be defined as the degree of connection between the various natural marine habitats, in terms of their species, spatial distribution and ecological functions. Over the years, the habitats have been modified and fragmented by human pressures and climate change. To offset the negative effects of fragmentation of natural habitats, conservation biologists have advised increasing connectivity between habitats. The conservation of natural corridors between habitats is essential to sustain biological diversity in a changing climate and to ensure the maintenance of ecological services to the community.

Dispersal is a key driver of marine population connectivity and crucial for population dynamics and gene flow. Hence, connectivity is believed to be important in determining how species will cope with e.g., a changing climate by allowing the ranges of species to expand or constrict in response to environmental shifts. Offshore structures such as wind farms are expected to affect the connectivity and spread of species to new areas in a stepping-stone effect. Connectivity analysis can also provide important information for site selection of nature restoration and marine protected areas.

Individual based models (IBMs) also called Agent-based models (ABMs), describe autonomous individual organisms or groups of organisms, each of them characterized by biological traits, which can interact with the environment using a unique set of behavioural rules. The dispersal pattern of the released particles (agents) can be used to assess the connectivity and spread of species. The modelling framework FlexSem is a fast, flexible and user-friendly tool specifically targeted towards scientific and management challenges of the complex coastal zone ecosystems. FlexSem is a modular marine modelling framework, containing a full 3D hydrodynamic module that can be couple with an ABM. The model code is open access and documented on the homepage https://marweb.bios.au.dk/FlexSem/. FlexSem will be the main tool for this course and ABM test cases will be provided on the student’s own pc’s (MacBooks are not supported).

Learning outcomes and competences:

At the end of the course, the student will be able to:

- Add an agent-based model to an existing FlexSem setup

- make initialization data and forcing data, and conduct scenarios

- add traits to the ABM

- make and plot output in R or Python

- be comfortable with 3D FlexSem modelling on your own pc

Course parameters:

Language:  English

Level of course: PhD and Post Doc course

Time of year: Jan 2025

No. of contact hours/hours in total incl. preparation, assignment(s) or the like: Contact: 21/50 hours

Capacity limits: 8

Course fee: 0

Compulsory programme:

Day 1:

• Welcome and agenda (Marie)
• Introduction to 3D modelling and the FlexSem framework (Janus)
• Set-up of FlexSem on pc’s (Janus)
• Run simple test case
• Make output plots

Day 2:

• Evaluation of test cases (problems, success, etc).(Janus)
• Examples of ABM studies with FlexSem (Vibe)
• Postprocessing and connectivity analysis (Vibe)
• Setup own test case
• Work on own test case and add traits

Day 3:

• Presentations of results from day 2 and discussions
• Get access to regional set-up (e.g., Inner Danish waters, Roskilde Fjord, North Sea)
• Course evaluation and goodbye

Course contents:

Lectures

Exercises

Individual project on different case studies

Prerequisites:

Some basic knowledge of R or Python

Bring your own pc (MacBooks are not supported).

Name of lecturers: Janus Larsen, Vibe Schourup-Kristensen, Marie Maar

Type of course/teaching methods:

Lectures and model exercises

Literature:

Schourup-Kristensen V, Larsen J, Maar M, Stæhr PU. (2023). Modeling the spreading of non-indigenous species in the Wadden Sea. Marine Environmental Research, 191: 106111. https://doi.org/10.1016/j.marenvres.2023.106111

Pastor A, Ospina-Alvarez A, Larsen J, Hansen FT, Krause-Jensen D., Maar M. (2022) A network analysis of connected biophysical pathways to guide eelgrass (Zostera marina) restoration. Marine Environmental Research 179:105690. https://doi.org/10.1016/j.marenvres.2022.105690

Pastor AR, Larsen J, Hansen FT, Simon A, Bierne N, Maar M (2021). Agent-based modeling and genetics reveal the Limfjorden as a well-connected system for mussel larvae. Mar. Ecol. Prog. Ser. 680:193-205. https://doi.org/10.3354/meps13559.

Larsen J, Mohn, C, Pastor AR, Maar, M (2020). A versatile marine modelling tool applied to arctic, temperate and tropical waters. PLoS One 15(4): e0231193. https://doi.org/10.1371/journal.pone.0231193

Course assessment:

Active participation and an individual report on the ABM implementation in personal regional set-ups and identified knowledge gaps finalized max 1 month after the training course.

Time: 20-22 January 2025

Place: Department of Ecoscience, Aarhus University, Frederiksborgvej 399, Roskilde 4000, Denmark

Course fee: none

Registration:

Deadline for registration is 11 December 2024. Information regarding admission will be sent out no later than two days later.

For registration: send an e-mail to Janus Larsen: janus@ecos.au.dk

If you have any questions, please contact Janus Larsen e-mail: janus@ecos.au.dk