1. Biodiversity in Pattern and Process

Below you find the available BSc and/or MSc projects available in the category "Biodiversity in Pattern and Process".

Synthesizing existing literature to gain insight into the habitat preference and behavior patterns of migratory butterflies in North, Central, and South America (BSc/MSc)

Supervisor(s): Edwin Pos
Project type: writing assignment
Starting period: flexible
Duration: flexible

Keywords: butterflies, migratory, habitat preference, behavior

The content of this project is to conduct an extensive search of scientific databases and literature sources to identify and analyze studies and research articles that relate to the habitat preference of migratory butterflies in North, Central, and South America and their wintering behavior. Methods will consist of extracting relevant data from the selected literature, such as information on plant species, nectar sources, climate conditions, and behavioral patterns of migratory butterflies. This data can then be analyzed to identify patterns and trends. Additionally, an examination of literature on the effects of human activities on migratory butterflies, such as habitat loss, climate change, and agricultural practices, and their impact on their behavior and habitat preference can be included. Results of this study will also feed into an aggregated database on butterfly characteristics, habitat preference and otherwise noteworthy data for public engagement and scientific studies.

Selected literature:

  • Chowdhury, Shawan, et al. "Migration in butterflies: a global overview." Biological Reviews 96.4 (2021): 1462-1483.
  • Thomas, Chris D. "Habitat use and geographic ranges of butterflies from the wet lowlands of Costa Rica." Biological Conservation 55.3 (1991): 269-281.

 

Synthesizing existing literature to gain insight of current status of discovery, threats and monitoring of frog populations of South and Central America and how both in- and ex-situ conservation can aid in safeguarding biodiversity (BSc/MSc)

Supervisor(s): Edwin Pos
Project type: writing assignment
Starting period: flexible
Duration: flexible

Keywords: frogs, ex-situ conservation, tropics

Worldwide, frogs are threatened in their existence. While new species are being discovered and on a global scale conservation efforts are being implemented, there are still gaps in our knowledge when it comes to how both in- and ex-situ conservation of amphibians should be combined towards a best practice of conservation, public outreach and education for safeguarding this biodiversity. In this literature project this will be the focus of study. The greenhouse of Utrecht University Botanic Gardens houses a number of species of frogs of South and Central America that might aid for ex-situ conservation. Simultaneously, collaboration with an association in Costa Rica gives the necessary foundation for in-situ conservation. Combining these efforts, supported with existing literature and a potential practical component monitoring frogs in the greenhouse should synthesize a growing database of frog conservation practices, combined with the necessary public outreach.

Selected literature:

  • Zippel, Kevin, et al. "The Amphibian Ark: a global community for ex situ conservation of amphibians." Herpetological Conservation and Biology 6.3 (2011): 340-352.
  • Michaels, Christopher J., Beatrice F. Gini, and Richard F. Preziosi. "The importance of natural history and species-specific approaches in amphibian ex-situ conservation." The Herpetological Journal 24.3 (2014): 135-145.
  • Caviedes-Solis, I. W., et al. "Everything is not lost: recent records, rediscoveries, and range extensions of Mexican hylid frogs." Mesoamerican Herpetology 2.3 (2015): 230-241.

Biodiversity cold spots, the forgotten areas of conservation (BSc)

Supervisor(s): Edwin Pos, Connor Smith, Kirsten Timmerman
Project type: internship or writing assignment
Starting period: flexible, but if experimental work is also desired P3-P4
Duration: flexible

Keywords: biodiversity, alpine flora, species distribution modeling, climate change

The idea of "biodiversity hot spots" has been well documented and is generally accepted within the scientific community. These areas of extreme biodiversity are usually centered around the equator. In the more temperate or alpine regions, however, it might be that there exist biodiversity "cold spots"; areas of major importance with regard to endemic diversity. In this project you will study biogeographical distributions of temperate, boreal and/or alpine (plant) species to identify such potential cold spots of biodiversity. In addition, you will develop species distribution models for some of these species or an ensemble to analyze their current potential distribution, to understand and model their environmental niche based on available information and generate predictions for consequences of future climate change. In addition, it might be possible to do a practical component involving a common garden experiment to test some of the results from the SDM approach regarding the climatic envelop.

Prerequisites: 

  • Nice-to-have: UU Course Spatial Evolutionary Ecology or similar

Selected literature:

  • Kareiva, Peter, and Michelle Marvier. "Conserving biodiversity coldspots: Recent calls to direct conservation funding to the world's biodiversity hotspots may be bad investment advice." American Scientist 91.4 (2003): 344-351.

Information based inference from strange attractors: the marriage between information entropy and chaos theory (MSc)

Supervisor(s): Edwin Pos, Fleur Slegers
Project type: internship or writing assignment
Starting period: flexible
Duration: flexible

Keywords: maximum entropy, non-linear dynamics, ecological dynamics

The principle of Maximum Entropy applied in ecology provides a top-down, unbiased, approach to infer understanding from complex, often multivariate data. With its origins in thermodynamics and statistical mechanics it provides a powerful tool to predict probability distributions using only so-called macrostate variables, such as the total number of species or individuals of an ecosystem. It is, however, also limited as currently it is mostly only applicable in a steady state manner, i.e. systems in which these state variables by approximation can be considered constant. For ecological systems, especially those that are disturbed this is not necessarily the case. Within the field of non-linear dynamics, principles from chaos theory potentially provide a novel way of to take into account changes of such state variables. There is, however, little known on the links between information inference methods, such as MaxEnt and chaos theory from the perspective of ecological systems. Questions that still remain are for example what variables are changing most in disturbed ecosystems, does this depend on the type of disturbance and once we know this – how can we best quantitatively describe the pattern of change to subsequently be of use in the Maximum Entropy framework? This is an explorative project, taking the first steps towards this integration and can be a literature study and/or practical project.

Prerequisites:

  • This project involves modeling and data analysis in R or python. Some experience with modeling therefore is required. In addition, this project has a strong theoretical component, affinity and experience in mathematical approaches is highly advised.

Selected literature:

Conservation theory of ecological entropy (MSc)

Supervisor(s): Edwin Pos
Project type: writing assignment
Starting period: flexible
Duration: flexible

Keywords: maximum entropy, ecological dynamics

The second law of thermodynamics states the entropy of any isolated system should increase over time, e.g. for those systems that do not exchange anything with the world outside of that system, it will evolve to a state of equilibrium often characterized by the absence of any gradient – the most uniform distribution. Simultaneously, all natural processes regardless of whether they are ecological, abiotic or otherwise are constrained by the very fundamental laws of nature such as the conservation of energy and mass, constituting the first law of thermodynamics. However, if we look at distributions of for example species abundance, biomass or metabolic energy of any ecosystem it is pretty much always skewed – far from uniform. Now, considering the earth being the closed system from the perspective of any smaller ecosystem residing on earth, one might consider that on a smaller scale any ecosystem can be seen as an open system, or even more specifically a so-called dissipative system. Such systems maintain order instead of disorder (i.e. a skewed distribution instead of a uniform one) by consuming free energy. How could the principles of thermodynamics be used to describe ecological processes? Is it possible to perceive ecosystems as thermodynamical systems obeying the very foundational rules of physics and thereby driving the patterns we observe in nature? This project aims at exploring this by reviewing current literature and pointing out knowledge gaps that require further study.

Prerequisites: This project has a strong theoretical component, affinity and experience in mathematical approaches is highly advised.

Selected literature:

  • Cushman, Samuel A. "Entropy, Ecology and Evolution Toward a Unified Philosophy of Biology." Entropy 25.3 (2023) 405
  • Nielsen, Søren Nors, et al. "Thermodynamics in ecology—An introductory review." Entropy 22.8 (2020) 820

Drought and Diversity: a quantitative in situ experiment near USP (BSc/MSc)

Supervisor(s): Edwin Pos, Yann Hautier
Project type: internship or writing assignment
Starting period: P1, P3 or P4 as there is fieldwork involved
Duration: flexible

Predictions of climate change suggest we will be facing more periods of severe drought, alternated with periods of more extreme precipitation. Near USP, a long-term monitoring experiment has started that will study the relationship between biodiversity and drought, combining various treatments of biodiversity with varying levels of simulated drought and high-resolution monitoring of soil moisture, temperature and conductivity as well as above-vegetation atmospheric temperature and humidity. The hypothesis is that higher levels of biodiversity potentially increase the buffering capacity of the soil to mitigate these effects of drought and the project simultaneously aims to quantify the trade-off between productivity and this relationship. In this project there is ample space for student involvement during peak times (e.g. spring and early summer) as well as literature studies throughout the year. Activities range from field collection, experimental analyses and subsequent processing of material as well as of course application of diverse statistical (multivariate) analyses.

Prerequisites: Experience doing ecological fieldwork is advised but not necessary. If this project is done for a BSc level project all practical experience can be acquired during the project. For a MSc. level project, the course VSR is a prerequisite.

Selected literature:

  • Hautier, Yann, et al. "General destabilizing effects of eutrophication on grassland productivity at multiple spatial scales." Nature Communications 11.1 (2020): 5375.TO BE DECIDED

Uncovering hidden patterns of tropical tree diversity in relationship to different land-use history (MSc)

Supervisor(s): Edwin Pos
Project type: internship
Starting period: P1
Duration: flexible, but it involves fieldwork.

Anthropogenic activities have radically altered our ecosystems, such as in tropical rainforests where human activities including (but not limited to) selective logging, forest burning or clearcutting are some examples. In terms of succession and forest regeneration, this project focusses on exploring the relationship between several different land-use history and tropical tree diversity. This project includes fieldwork in Costa Rica at the facilities of Adopteer Regenwoud during which forest inventories take place. Take into account that this project requires a strong work ethic, preferably experience in fieldwork (not in the tropics perse) and will require covering some costs yourself, such as travel and accommodation. It will, however, also provide a unique experience and there are opportunities to apply for (external) student grants with foundations such as Kronendak, Alberta Mennega stichting and het Van Eedenfonds.

Prerequisites: Experience doing ecological fieldwork in general is advised but not necessary, the course VSR is a prerequisite. Experience with spatial modeling could be beneficial depending on the scope of the project but is not required.

Selected literature:

  • Poorter, L., Rozendaal, D. M., Bongers, F., Almeida, D. J. S., Álvarez, F. S., Andrade, J. L., ... & Westoby, M. (2021). Functional recovery of secondary tropical forests. Proceedings of the National Academy of Sciences, 118(49), e2003405118.
  • Rozendaal, Danaë MA, et al. "Biodiversity recovery of Neotropical secondary forests." Science advances 5.3 (2019): eaau3114.
  • Borges, Erica R., et al. "The interaction of land-use history and tree species diversity in driving variation in the aboveground biomass of urban versus non-urban tropical forests." Ecological Indicators 129 (2021)- 107915

The effects of habitat (de)fragmentation and dispersal on METE’s species abundance distribution estimation (BSc/MSc)

Supervisor(s): Monique de Jager
Project type: internship or writing assignment
Starting period: flexible
Duration: flexible

Keywords:  Maximum entropy theory in ecology, Community dynamics, Individual-based modelling

    With maximum entropy models, the species abundance distribution pattern of a healthy community can  be quite accurately described. Many communities are, however, not in a healthy state, as they are experiencing the effects of anthropogenic changes. One of these changes to the environment is severe habitat fragmentation. Due to habitat fragmentation, dispersal between communities becomes more difficult. Such dispersal limitation impairs gene flow and colonization by new species, amongst others. Furthermore, habitat fragmentation reduces population size and thereby can have additional effects, such as increasing genetic and ecological drift. To estimate the state of communities and their level of fragmentation, we examine changes in METE’s prediction of the species abundance distribution of simulated data. Using a simple individual-based model, we simulate community assembly and dynamics under changing fragmentation conditions.

    Prerequisites: 

    • This project involves modeling and data analysis in R (potentially rewriting the script to C++ or python). Some experience with R is required.

    Selected literature: 

    The eco-evolutionary effects of habitat fragmentation and restoration on animal movement strategies (MSc)

    Supervisor(s): Monique de Jager
    Project type: internship
    Starting period: flexible
    Duration: flexible

    Keywords:  Animal search strategies, evolution, Individual-based modelling

    In my 2023 Ecology and Evolution paper, I demonstrated that changing habitat fragmentation levels can cause evolutionary hysteresis in the dispersal capacity of water-dispersed plants. In this student project, we will investigate how increasing and decreasing habitat fragmentation levels change optimal animal search strategies. Using an individual-based model, students can focus on a wide range of parameters that may change the outcome of the model simulations.  

    Prerequisites: 

    • This project involves modeling and data analysis in R (potentially rewriting the script to C++ or python). Some experience with R is required.

    Selected literature: 

    • De Jager & Soons (2023) Critical transitions and evolutionary hysteresis in movement: Habitat fragmentation can cause abrupt shifts in dispersal that are difficult to revert. Ecology and Evolution. doi: 10.1002/ece3.10147
    • De Jager, Buitendijk, Baveco, van Els  & Nolet (2023). Limiting scaring activities reduces economic costs associated with foraging barnacle geese: Results from an individual-based model. Journal of Applied Ecology 60, 1790-1802.

    Perfecting the model: does adding more realistic grass growth affect the results of the barnacle goose foraging model? (MSc)

    Supervisor(s): Monique de Jager
    Project type: internship
    Starting period: flexible
    Duration: flexible

    Keywords:  Grass growth, goose grazing, farmer-wildlife conflict, individual-based modelling

    With an individual-based model of barnacle geese foraging on grasslands in the province Friesland, we showed that no management is the best management when it comes down to minimizing economic costs. In this model, grass growth is highly simplified. Using data collected in field experiments, grass growth can be modeled more realistically. Will such an extension affect the results?

    This project involves data analysis in R, modeling in C++, and collaboration with the Netherlands Institute of Ecology (NIOO-KNAW).

    Prerequisites: 

    • Experience with R is required.

    Selected literature: 

    • De Jager et al. (2023) More grazing, more damage? Assessed yield loss on agricultural grassland relates nonlinearly to goose grazing pressure. Journal of Applied Ecology 60:1790–1802.
    • Buitendijk & Nolet (2023) Timing and intensity of goose grazing: Implications for grass height and first harvest. Agriculture, Ecosystems & Environment 357: 108681.