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Tree and Fossil Generators

Winter 2022 ~ @TitouanCh
Simple tool to generate tree and fossil data...

Pause :

Ntips :
Speciation (λ) :
Extinction (µ) :
Extant Sampling (ρ) :
Fossil Recovery (Ψ) :

The importance of fossils

The fossil record is crucial for understanding how life has evolved over time. It helps us see big patterns in evolution, like how species have diversified and when key events in Earth's history happened. Fossils also play a big role in figuring out how different species are related to each other. This has led scientists to develop models that can include information from fossils when studying evolutionary relationships.

Ammonite depicted from fossil
How scientists believed ammonite looked from fossil data in 1908

The challenges of working with fossil data

Studying fossils is tricky because they're often incomplete and not evenly spread out. This means we have to be careful when interpreting what fossils tell us about ancient species and how they evolved. Current models used in research often simplify the process of how fossils are found and how species change over time. To improve our understanding, scientists use computer simulations to test different distribution of fossil data under various conditions. These simulations help them see how well their models work and what limitations they might have.

My model

Here I've implemented one such model. Using different parameters you can simulate phylogenetic and fossil data and imagine what the reconstructed tree would have looked like (hint: the reconstructed tree often looks quite different from reality).

This sort of model give us great insights into the pitfalls we can encounter when reconstructing trees. Implemented in javascript using a foward generating method, my fairly simple model can still highlight some biases.

For further exploration on this topic, I recommend taking a look at the R package FossilSim and its app FossilSimShiny. They provide powerful tools for simulating and visualizing evolutionary scenarios.