Examples gallery
Click any figure for the code that produces it. Every example simulates with ZOMBI2 and plots with Phylustrator, a separate package — so to run one you need both:
pip install zombi2 phylustrator
Species trees
6Forward birth-death trees. The run keeps the whole history, survivors and extinctions, and the diversification model shows on the tree.
Yule tree
Pure birth, no extinction — a forward tree of 100 lineages.
pure birth (Yule)
Extinct lineages
The full history behind 50 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 · + skyline
Shape statistics over many trees
Two thousand trees under each of two processes. zombi2 tools tree --gamma separates them almost perfectly.
Genomes
9Genes on chromosomes. A genome draws as a ring, and two genomes show their synteny. 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().
Synteny across a whole clade
Every tip's gene order beside the tree. Genes are coloured by their ancestral position, so each rearrangement is a break in the gradient.
phylustrator · synteny
Gene-family events on the tree
One family's history on the species tree: duplications (squares), losses (crosses), transfers (arrows, donor→recipient).
phylustrator · 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. The forward/reverse switch marks the replication origin.
phylustrator · real GFF
An inversion, before → after
One inversion on a circular genome: the segment is reversed and its strands flip. The band marks it in both rings.
phylustrator · circular
A transfer highway between clades
Transfers steered to run between two clades, by topology rather than by a trait. The barplot counts them by clade pair, so A↔B towers over within-clade.
clades · transfer_to
Core and accessory, from one parameter
Two runs at the same mean rates. Every family alike gives no core at all; letting families differ gives 28 core families and a U-shaped spectrum.
phylustrator · heterogeneitySequences
6The dated tree the sequences evolve down, and an alignment lined up row-for-row with its tips.
Uncorrelated lognormal clock
Every lineage draws its own rate, with no memory of its parent, so the colour is salt-and-pepper. substitution = PerSite().varying_among('lineages', LogNormal(0.0, 0.55)).
Uncorrelated gamma clock
The same independent draw with a gamma instead of a lognormal. varying_among('lineages', Gamma(shape=3.31, scale=0.302)).
Autocorrelated clock
A daughter starts at its parent's rate and is nudged, so the colour moves in clades rather than branch to branch. substitution = PerSite().varying_among('lineages', Drift(LogNormal(0.0, 0.4))).
Discrete-bin clock
The same inherited drift in steps: the rate takes one of a few values and a daughter moves to a neighbouring one. varying_among('lineages', Drift(LogNormal(0.0, 0.45), bins=6)).
Ancestral sequences at the nodes
A small tree with its internal nodes numbered, and beside it the sequence at each. The rows are one per node, not aligned to the tips.
phylustrator · ancestral
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)).
Traits
6A trait evolving down the tree. Branches take the colour of its value. Some examples add 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
Dependent continuous traits
Two traits evolve together (r = 0.9) — two trees, coloured by each trait, and the tip scatter.
continuous · + scatter
Dependent discrete traits
Two binary characters where one's flip rate depends on the other's state. X in green, Y in purple, so you can see Y is present where X is; the 2×2 chain is the model.
discrete · dependent
A trait driving a trait
A habitat trait sets how fast body size diffuses: twenty times faster where the habitat fluctuates. rate = PerLineage(0.25).scaled_by(habitat, {…}).
Conditioning
9Two runs, in order. The first run grows the driver on the tree and holds it fixed. The second run reads it. A driver is a trait, a gene family or a whole module. It drives a rate, or which lineage receives a transfer.
Genome reduction
A lifestyle trait drives gene loss. Endosymbionts shed genes faster and gain fewer, so their genomes end up a fifth the size.
trait → loss
Genome expansion
A selection trait drives duplication. Under relaxed selection duplicates accumulate and the genomes grow fivefold.
trait → duplication
HGT uptake by competence
A competence trait drives who receives a transfer rather than a rate. Competent lineages take up DNA more often.
trait → transfer uptake
A continuous driver
A diffusing trait drives gene gain. A Curve turns each value into a factor, so genome size follows the trait.
A saturating curve
The same run with a different Curve. Gene gain rises with the trait and then levels off, so the factor is bounded.
A curve of your own
The response is any function you write. Here it peaks at an intermediate value, which no table of per-state multipliers can express.
continuous trait → origination
One trait drives another
A temperature trait is grown first; body size then diffuses at a rate that reads it. The scale is centred on where it started, so white means it has not moved.
trait → trait
A gene drives a trait
Carrying a toxin family makes a lineage become pathogenic forty times faster. 74% of the tips with the gene end up pathogenic, against none of those without.
gene → trait
A module, through a step
How much of a four-gene module a lineage keeps decides its metabolism, through a step: lambda f: 20.0 if f > 0.5 else 1.0.
Joining
3One run makes both. The trait sets the speciation or extinction rate of the lineage carrying it. The trait and the tree therefore come out together.
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