BIOL 108 Final Project – Late Devonian Biodiversity Loss

Project Concept

This project explores genus-level biodiversity loss during the Late Devonian extinction, with a focus on marine invertebrates. The main goal is to use real fossil occurrence data to find patterns in extinction intensity across time and taxonomy.

While paleontology isn’t a subject I’ve gravitated toward naturally, I do enjoy coding and data work. This project felt like a good opportunity to bring Python into the mix and make the material more engaging.

Format

I’m presenting the project in the form of a Jupyter Notebook that combines:

• Markdown narration for structure and explanation
• Python-based data analysis (mostly using pandas and matplotlib)
• Visualizations to highlight trends in the dataset

Core Questions

1. Is there measurable evidence of biodiversity loss during the Kellwasser (372 Ma) and Hangenberg (359 Ma) extinction events?
2. How severe were these extinction events at the genus level, and how do those patterns compare to species-level trends in the same time intervals?
3. Can observed patterns be explained by sampling bias or uneven fossil record coverage in the Paleobiology Database (PBDB)?

Data Sources

• Fossil occurrence data from the Paleobiology Database (PBDB)
• Local files: Genus.csv, Species.csv, Family.csv

Planned Notebook Structure

1. Introduction

   • Context and background on the Late Devonian extinction
   • Why it’s relevant in the history of biodiversity

2. Data Preparation

   • Load and clean the datasets
   • Standardize taxonomic names
   • Filter records to the Devonian period

3. Biodiversity Metrics

• Genus vs species richness through time
• Comparison of extinction timing and severity across taxonomic levels

4. Visual Analysis

   • Time series and bar plots
   • Optional breakdowns by taxonomy or ecology

5. Interpretation

   • Patterns in diversity loss
   • Discussion of possible drivers (e.g., sea level changes, ocean anoxia)

6. Conclusion

   • Summary of findings
   • Reflection on what data science can bring to paleobiology

Reflection Piece

The reflection will explain why I chose to approach the topic through coding, and how this method helped make the research more meaningful. It’ll also connect the work back to core course themes—like evolutionary relationships, environmental context, and fossil preservation.