Phylogenetics 101 — Part A

Core Idea (bird's-eye view)

A phylogenetic tree is a hypothesis about evolutionary relationships among taxa, inferred from data (never directly observed). This practical is about how trees are represented as text files (Newick, Nexus) and the structural rules/math behind them. You need to be fluent in reading a tree string, counting its parts, and knowing why two strings can describe the same tree.

Key conceptual anchors from theory you must carry into the practical:

• Tree = topology + (optionally) branch lengths. Topology = branching pattern only.
• Cladogram (topology only) vs phylogram (branch length = evolutionary change) vs chronogram (branch length = time).
• Rooted vs unrooted: rooting gives direction (time) to the tree. Done via outgroup or midpoint.
• Clades: monophyletic (ancestor + ALL descendants), paraphyletic (ancestor + SOME descendants), polyphyletic (multiple ancestors, misleading group).
• Synapomorphy = shared derived trait → defines clades. Symplesiomorphy (shared ancestral) is misleading.
• Nodes = ancestors (internal) or OTUs/tips (terminal). Branches connect them. Polytomy = unresolved node with >2 descendants.
• A tree is NOT a ladder — no taxon is "more advanced"; relatedness comes from MRCA, not tip order.

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Inputs

The practical works on tree files as text. The two formats:

1. Newick (.nwk)

A nested-parenthesis string. Building blocks: ( ), ,, :, names, numbers, terminating ;.

Examples (increasing complexity):

(,(),(,));                              no names
(A,(B,(C,D)));                          leaf names only
(A,(B,(C,D)E))F;                        all nodes named
(A:0.1,(B:0.2,(C:0.3,D:0.4):0.5));      names + branch lengths

Polytomy vs dichotomy:

(A,B,(C,D));        polytomy at root
(A,(B,(C,D)));      fully dichotomous

2. Nexus (.nex)

A structured file with blocks (BEGIN ... END;). Header is #NEXUS. Common blocks:

• TAXA — list of taxon labels
• CHARACTERS / DATA — character matrix (DNA, morphology, etc.)
• TREES — contains one or more trees written in Newick format internally

#NEXUS
BEGIN TREES;
  TREE tree1 = ((A,B),(C,D));
END;

So Nexus is the flexible container, Newick is the tree-string syntax that lives inside it (or alone).

Tools to view them

• FigTree (GUI), or online viewers — visualize .nwk / .nex.

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Outputs

The practical doesn't really "produce" data — the outputs are:

• A rendered tree in FigTree (or similar) from a Newick/Nexus string.
• Your ability to count branches/nodes for a given N tips.
• Recognition that multiple Newick strings = the same tree (rotations are free).

The counting formulas (memorize — likely exam fodder)

For an unrooted tree with N tips:

Quantity	Formula
Terminal branches	N
Total branches	2N − 3
Internal branches	N − 3
Internal nodes	N − 2

Number of possible trees explodes:

• A rooted tree has 2N − 3 times as many possibilities as the unrooted equivalent.
• 10 leaves → ~2 million unrooted, ~34 million rooted.

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Interpretations

• Same tree, different strings: (A,B,(C,D)); ≡ (B,A,(C,D)); ≡ ((C,D),A,B); ≡ (A,B,(D,C));. Any internal node can be rotated without changing the topology. Don't be fooled by tip order.
• Different trees look superficially similar but differ in their bipartitions/splits (which taxa are grouped together). For 4 taxa: only 3 distinct unrooted topologies exist → AB|CD, AC|BD, AD|BC.
• Branch length meaning depends on tree type: in a cladogram lengths are arbitrary; in a phylogram they = substitutions/site; in a chronogram they = time.
• A polytomy ≠ a real burst of speciation necessarily — usually it means unresolved relationships in the data.
• Reading relatedness: trace back to the most recent common ancestor (MRCA). Adjacency at the tips means nothing.

Common pitfalls of Newick (the prof may quiz these)

• Must end with ;
• Parentheses must balance
• Either give branch lengths everywhere or nowhere
• Special chars in names → quote: 'Homo sapiens'
• Whitespace is ignored; trees can wrap across lines

Possible Exam Questions

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60-second mental cheat sheet

• Newick = string with ( , ) ;. Nexus = #NEXUS file with BEGIN ... END; blocks containing Newick trees.
• N tips → N−2 internal nodes, 2N−3 total branches, N−3 internal branches.
• Rotation of internal nodes = SAME tree.
• 4 taxa → only 3 unrooted topologies.
• Cladogram (shape) → Phylogram (change) → Chronogram (time).
• Mono / Para / Poly — know the diagram.
• Synapomorphy defines clades. Symplesiomorphy misleads.
• A tree is a HYPOTHESIS, never a fact.