A diversification simulator for lineage history, coarse-grained taxa, and trait-based tree reconstruction.
Static HTML app for exploring budding lineages, species-level coarsening, extinction, and how trait summaries can disagree with event history.
EvoLab is an interactive teaching and exploration tool built around a continuous-time budding diversification process.
- Each extant lineage can produce a clonal daughter, produce a mutating daughter, or go extinct.
- The simulator tracks the full lineage record through time rather than jumping straight to a final tree.
- A coarsening rule turns lineage-level events into observed "species" by requiring a chosen number of mutational steps before naming a new taxon.
- The same run is then shown through linked views: full history, coarsened chronogram, history tree, trait tree, lineages through time, and trait space.
For the full discussion and interpretation, see the blog post.
| Control | Visualizations |
|---|---|
 |
 |
evolab.html: the whole simulator in one file- Seeded preset scenarios for balanced exploration, high turnover, rapid radiation, and OU-like trait constraint
- JSON export for complete run history
- Newick export for the history tree and the trait tree
- Light and dark display support
git clone https://github.com/EvoLandEco/EvoLab.git
cd EvoLabBrowsers handle clipboard features more reliably over http:// than file://, so run a tiny local server from the repo root:
python -m http.server 8000http://localhost:8000/evolab.html
The page loads D3, numeric.js, Bootstrap, and Font Awesome from public CDNs, so the browser session needs internet access unless you vendor those files locally.
Each run starts with one lineage. Event times are sampled in continuous time with a Gillespie-style stochastic simulation algorithm. At each event, one extant lineage is chosen and one of three outcomes happens:
- Clonal birth: a daughter lineage inherits the parent's trait vector
- Mutating birth: a daughter lineage receives a trait step and may contribute toward a new observed taxon
- Death: the lineage is marked extinct and stops participating in later events
Observed taxa are built from the lineage record by a coarsening rule:
- At coarsen level 0, every new lineage can become a named taxon right away
- At higher coarsen levels, mutational steps must accumulate before a new taxon is recorded
The simulator then derives:
- A full lineage chronogram
- A coarsened species chronogram
- A history tree from the coarsened event table
- A trait tree built from observed trait distances with UPGMA
- A lineages-through-time summary
- A trait-space view using the first two trait axes or PCA when needed
- Pick a preset or enter your own rates.
- Set the step limit and coarsen level.
- Choose a trait model:
- Brownian steps for unconstrained wandering
- OU-like pull for movement toward an optimum
- Press Grow to animate the run, or Step to inspect the process one event at a time.
- Use Export JSON, Copy history Newick, and Copy trait Newick when you want to reuse a run elsewhere.
EvoLab uses:
- D3.js for the interactive graphics
- numeric.js for the PCA fallback
- Bootstrap for interface primitives
- Font Awesome for UI icons
MIT License.