Student projects

If you are interested in:

please get in touch about possible student projects. We offer: training, intensive supervision with many contact hours, a closely-knit team, potential contribution to a publication and tailoring to different study and career paths.

Reconstructing spatial changes in the Bahamas

The Bahamas are THE carbonate platform, a classic sandbox for all carbonate sedimentologists and marine ecologists studying tropical environments. Models of reef growth and sediment formation originate from the Bahamas. They are a fantastic case for studying the interaction between organisms and the marine and terrestrial landforms. Corals, algae, mangroves and seagrass are ecosystem engineers, which transform the seabed and the coastline, stabilizing it and creating spatial patterns reflecting their habitat and dispersal.

But one element is missing: the temporal aspect. We know how the organisms and environments are distributed today, but how fast do they move? We have secured access to a unique archive of the first aerial photographs of the Bahamas, dating back to the forties, and digitized them in collaboration with Sam Purkis (Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami).

The goal of the project is to quantify how the spatial distribution of environments changed at the time scale of a century.

We expect that you spend part of your project doing analysis using image processing software and are willing to read up textbook material about carbonate sedimentology and geomorphology appropriate to your study level.

Contact: Xianyi Liu and Emilia Jarochowska

Introductory Reading

  • Harris, Paul M. (Mitch), Samuel J. Purkis, and James Ellis. 2011. "Analyzing Spatial Patterns in Modern Carbonate Sand Bodies From Great Bahama Bank." Journal of Sedimentary Research 81 (3): 185–206. https://doi.org/10.2110/jsr.2011.21.

  • Rankey, Eugene C., and Jim Morgan. 2002. "Quantified Rates of Geomorphic Change on a Modern Carbonate Tidal Flat, Bahamas." Geology 30 (7): 583–86. https://doi.org/10.1130/0091-7613(2002)030<0583:QROGCO>2.0.CO;2.

  • Violette, Clémentine, Mehdi Adjeroud, Claude Payri, Sam J. Purkis, and Serge Andréfouët. 2024. "Changes of Tiahura (Moorea Island) Reef Flat Habitats Using 67 Years of Remote Sensing Observations." Coral Reefs, October. https://doi.org/10.1007/s00338-024-02576-8.

Find the Gap: Distribution of gap durations and locations in carbonate systems

The rock record is a key source of information to understand the Earth’s history, ranging from climate change over biotic interactions to evolution. Being a part of the rock record, the fossil record is incomplete, as parts of it are destroyed by erosion or not formed in the first place, thus resulting in gaps (hiatuses) in the record. Understanding where such gaps occur and how long they are is crucial if we want to use the fossil record to understand past changes. We know that gaps in the rock and/or fossil record are not random, but determined by a combination of drivers, such as sea level, insolation, and biotic interactions.

In this project, you will use an Open Source forward computer model (CarboKitten.jl) developed in collaboration between Utrecht University and the Netherlands eScience Center to simulate carbonate platforms under different external drivers of platform growth to explore how these drivers determine the position and duration of hiatuses.

You will:

  • learn how to program in Julia, a new programming language developed specifically for scientific computing,
  • how to run forward models of carbonate platform growth in it,
  • collaborate with a diverse team, including Research Software Engineers from the eScience Center and international scientists,
  • develop transferable IT skills: version control and collaborative coding using git, data visualization, reproducible research, optionally: automating research workflows

The results of your project will contribute to a scientific publication.

Possible formats: Masters thesis, guided research project, internship. The work can be completed remotely or fully on site. We offer regular meetings with you and support by dedicated Software Engineers.

Contact: Niklas Hohmann, Xianyi Liu and Emilia Jarochowska

Introductory Reading

  • Davies, Neil S., Anthony P. Shillito, and William J. McMahon. 2019. "Where Does the Time Go? Assessing the Chronostratigraphic Fidelity of Sedimentary Geological Outcrops in the Pliocene–Pleistocene Red Crag Formation, Eastern England." Journal of the Geological Society 176 (6): 1154–68. https://doi.org/10.1144/jgs2019-056.

  • Hohmann, Niklas, Joël R. Koelewijn, Peter Burgess, and Emilia Jarochowska. 2024. "Identification of the Mode of Evolution in Incomplete Carbonate Successions." BMC Ecology and Evolution 24 (1): 113. https://doi.org/10.1186/s12862-024-02287-2.

  • Tomašových, Adam, Ivo Gallmetzer, Alexandra Haselmair, and Martin Zuschin. 2022. "Inferring Time Averaging and Hiatus Durations in the Stratigraphic Record of High-Frequency Depositional Sequences." Sedimentology 69 (3): 1083–1118. https://doi.org/10.1111/sed.12936.

Stratigraphic Paleobiology in Carbonate Platforms

Context

Last occurrences of fossil taxa are of great importance for paleontologists. In biostratigraphy, they provide important information about relative ages of rocks and outcrops. Clusters of last occurrences indicate a mass extinction, potentially due to rapid environmental changes (e.g. climate change, volcanic eruptions, widespread anoxia).

Cretaceous carbonate platform at Miravete, Spain

However, this is not the only explanation for last occurrences. Every taxon lives only in specific environments, characterized by specific environmental conditions (water depth, light availability, substrate consistency, wave energy etc.). Taxa will migrate in space and time with their preferred living conditions (their niche). Last occurrences observed on the fossil record do not necessarily correspond to the extinction of a taxon, but can also be a result of local changes in environmental conditions that result in the taxon disappearing locally.

Project goal

The effect of taxa tracking their niche on last occurrences has been studied extensively by Holland & Patzkowsky (2012). However, their work focuses on siliciclastic systems. The aim of this project is to exapand upon their work by translating it to carbonate systems, which form the majority of the tropical fossil record.

In this project, the CarboKitten.jl or CarboCAT models (Burgess 2013) will be used to simulate carbonate platforms and track environmental conditions with time. The outputs will be combined with species niche modeling in R using the StratPal package to generate a synthetic fossil record, and examine how last occurrences systematically change along an onshore-offshore gradient and across facies boundaries and hiatuses.

Skills and Knowledge

During the project, you will learn the following skills:

  • Basin modeling

  • Species niche modeling and data analysis in R

  • Literature research using Zotero and researchrabbit

  • Version control using Git and GitHub

  • Scientific writing

You will acquire knowledge about the following topics:

  • Stratigraphic paleobiology

  • Ecological niche models

  • Carbonate sedimentology

Requirements

Basic coding skills in any modern programming language. It is not necessary to be familiar with R or Python, but some readiness to learn is needed. You will not have to write code from scratch (unless you want to), but work with existing code and modify it to your needs.

References

  • Holland, S.M. and Patzkowsky, M.E. (2015), The stratigraphy of mass extinction. Palaeontology, 58: 903-924.

  • Kidwell, Susan M., and Steven M. Holland. “The quality of the fossil record: implications for evolutionary analyses.” Annual Review of Ecology and Systematics 33.1 (2002): 561-588.

  • Patzkowsky, Mark E., and Steven M. Holland. “Stratigraphic paleobiology.” University of Chicago Press, 2012.

  • Burgess, Peter M. “CarboCAT: A cellular automata model of heterogeneous carbonate strata.” Computers & geosciences 53 (2013): 129-140.

Contact: Niklas Hohmann and Emilia Jarochowska

Orbital Controls of Coral Growth

Reefs are important paleontological archives that provide insights into past life and climate. One of the major controls on reef growth is energy provided in the form of sunlight. Over geological timescales, energy input is changing systematically due to periodic variations in the earth’s orbit around the sun (Milankovitch cyclicity). This orbital forcing is a major driver of climate change and source of information to derive age constraint for evolutionary studies. As a result, archive and signal are coupled, creating the potential for non-linear feedbacks and biases on how past climate is reconstructed.

The goal of this project is to study this feedback, specifically how

  • carbonate production is influenced by spatial and temporal variations of insolation

  • insolation driven variability in carbonate production changes the structure of stratigraphic columns and, in turn, inferences on orbital forcing drawn from them.

For this, insolation values from the palinsol package for the R software will be combined with the carbonate growth model from Boscher & Schlager (1992) to generate synthetic carbonate stratigraphies. These will be compared with each other to examine how they differ through time and space, and the approach from Kemp et al. (2016) will be used to examine under which circumstances the original orbital signal can be recovered from them.

Introductory reading

  • R package palinsol

  • Bosscher, Hemmo, and Wolfgang Schlager. “Computer simulation of reef growth.” Sedimentology 39.3 (1992): 503-512.

  • Kemp, David B., et al. “Investigating the preservation of orbital forcing in peritidal carbonates.” Sedimentology 63.6 (2016): 1701-1718.

  • Dullo, Wolf-Christian. 2005. "Coral Growth and Reef Growth: A Brief Review." Facies 51 (1): 33–48. https://doi.org/10.1007/s10347-005-0060-y.

The memory of the stratigraphic record

Successions of facies are commonly modeled via transition matrices that describe the transition probabilities / rates between facies. This assumes that the stratigraphic record is memorylessness and can thus be modeled via a Markov chain. The aim of the project is to test this assumption. A stratigraphic record with a longer memory can be modeled as a Markov chain of n-th order after expanding the state space. In the project, the student will assess how memory length of Markov chain models affects the capability to explain empirically observed stratigraphic successions.

Introductory reading

Other topics

  • Study taphonomy across the agronomic revolution using the PartiMoDe model

  • Preservation of Regime Shifts, Resilience, and Recovery in Modern Marine Environments