Examples gallery
Short, runnable recipes — each simulates with ZOMBI2 and plots with Phylustrator. Click any figure for the code and a short explanation. The levels of a run: species, genomes, sequences, traits, and the joining that couples them.
◆ Every figure is built from a real ZOMBI2 run — the code shown reproduces it.
Species trees
5Forward birth–death trees — the whole history, survivors and extinctions, with the diversification model made visible.
Yule tree
Pure birth, no extinction — a forward tree of 100 lineages.
pure birth (Yule)
Extinct lineages
The full history behind 100 survivors — their branches solid, extinct lineages dashed.
birth–death
Mass extinction
A pulse at t = 3 culls 75% of lineages — the skyline drops sharply at the dashed line, then recovers.
mass extinction · + skyline
Rate shifts
Speciation runs slow, then fast, then slow — the burst packs branches between the two dashed regime lines.
time-varying birth
Diversity-dependent
Speciation slows as diversity fills up; the skyline rises and plateaus at the cap of 100.
birth–death · + skylineGenomes
5Genes on chromosomes — a genome as a ring, synteny between genomes, and gene-family events and copy number read against the species tree.
Circular genome (ordered)
A genome as a ring — genes evenly spaced by rank, coloured by family, arrows by strand. plot(g, layout="circular") + genes().
Synteny between two genomes
Two genomes, one per row; ribbons link same-family genes and cross where the order was rearranged. stack([a,b]) + synteny().
Gene-family events on the tree
One family's history on the species tree: duplications (squares), losses (crosses) and transfers (arrows, donor→recipient). plot(tree) + branch_events(…).
Profile copy-number
A family × genome copy-number heatmap, its rows locked to the tips. beside(tree, heatmap(profiles)).
Real genome (Mycoplasma)
A real bacterium — Mycoplasma genitalium, 546 genes at their true base positions, coloured by strand; the forward/reverse switch marks the replication origin. read_gff(…).
Sequences
2The dated tree the sequences evolve down, and an alignment lined up row-for-row with its tips.
Sequence phylogram
The clock tree the sequences evolve down — branch lengths are substitutions/site under an uncorrelated relaxed clock, so the tips are not level.
phylustrator · phylogram
Alignment beside the tree
A single-copy family across 20 species, residues coloured (with a nucleotide key), each row locked to its tip. beside(tree, alignment(aln)).
Trait evolution
5A trait evolving down the tree — branches coloured by its value; some paired with a companion panel.
Brownian motion
Free diffusion — sister lineages drift apart with time.
continuous
Ornstein–Uhlenbeck
Pulled to an optimum: a high start (yellow) converges to blue.
continuous
Discrete states
A two-state trait hops between habitats; each branch is painted by its state history.
discrete · Mk
Correlated traits
Two traits evolve together (r = 0.9) — two trees, coloured by each trait, and the tip scatter.
continuous · + scatter
Dependent characters
Two binary characters where one's flip rate depends on the other's state — the model as a 2×2 chain (arrow width = rate), and a run: the tree painted by compound state, beside the presence/absence tips. simulate_discrete(states=("00",…), switch={…}).
Joining
3A trait and the tree grow together — the trait drives diversification, so its state shapes the tree.
BiSSE
A two-state trait drives speciation — the fast state's clades take over; the inset is the state Markov chain.
trait → speciation
State-dependent extinction
One state dies far faster; the doomed lineages (dashed) drop out.
trait → extinction
MuSSE
Three graded speciation rates with constant death — the fastest state fills the tree, extinct lineages dashed.
trait → speciation