Related Experiment Video
Updated: Jun 12, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data
Sophie Seidel1,2, Antoine Zwaans3,4, Samuel Regalado5
1Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. soseidel@uw.edu.
Nature Communications
|June 10, 2026
Summary
CRISPR lineage tracing now has a powerful tool, SciPhy, for reconstructing cell family trees. This Bayesian phylogenetic approach accurately models cell populations and developmental dynamics.
Area of Science:
- Genetics
- Computational Biology
- Developmental Biology
Background:
- CRISPR-based lineage tracing enables single-cell lineage tree reconstruction, particularly in challenging organisms.
- Sequential genome editing captures both genetic modifications and their temporal order.
Purpose of the Study:
- Introduce SciPhy, a novel simulation and inference tool for CRISPR lineage tracing data.
- Leverage Bayesian phylogenetics to jointly estimate phylogenies and cell population dynamics.
Main Methods:
- SciPhy is implemented in BEAST 2, employing a Bayesian phylogenetic approach.
- The tool was validated using simulated data and benchmarked against existing methods with real data.
Main Results:
- SciPhy accurately reconstructs phylogenies from CRISPR lineage tracing data.
- It outperforms UPGMA, providing estimates of uncertainty and proliferation rates.
- The tool successfully models time-varying population dynamics in murine gastruloids.
Conclusions:
- SciPhy establishes a robust phylodynamic framework for quantitative lineage tracing analysis.
- This tool enhances the study of cellular development and population dynamics.
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