Tutorial 3: Discrete biogeography of simulation study
In this tutorial, we'll apply what we learned in Tutorial 2 and 3 to a discrete biogeography dataset. This is ancestral range reconstruction was inferred for Malesian Rhododendron section Vireya using BayArea (http://bayarea.googlecode.com).
####Part A: Getting started
- Open the vireya dataset as explained in the Quick Start section.
- Play the animation.
- Notice how multiple areas may be occupied by a single lineage, forming a range. This is definitive of biogeographical analyses in Phylowood.
- If your animation is playing, click the Pause button. Reposition the slider to around -22 Myr. The timer above the phylogeny corresponds to the slider position.
####Part B: Highlighting controls
- Position the mouse over a marker on the map or over a branch on the phylogeny.
####Part C: Masking controls
- Mask lineages so only markers of interests are allocated area for display on the map. This is useful when you would like have very low lineage-per-area density.
- Double-click a branch to mask the lineage's continuum (i.e. the root).
- Single-click a branch to unmask the lineage's continuum (i.e. the lineage anticipating a clade).
- Single-click any other branches of interest. (This image shows a paraphyletic group.)
- Finally, single-click the root branch to unmask all the lineages.
