Phylogeny and Cladistics

Phylogeny is the study of the evolutionary relationships between species. Where classical classification was content to group organisms by similarity, modern phylogenetics asks a deeper question: which species share a common ancestor, and how recently? Phylogenetic trees are the answer, and the discipline of cladistics provides the rules for building them. OCR A-Level Biology A specification 4.2.2 (e)–(f) requires you to interpret phylogenetic trees and to understand the molecular evidence used to construct them.

Key Definitions:

• Phylogeny — the evolutionary history and relationships of species.
• Phylogenetic tree — a branching diagram showing evolutionary relationships.
• Cladistics — a method of classifying organisms based on shared derived characteristics.
• Clade — a group of organisms that share a common ancestor (a monophyletic group).
• Common ancestor — an ancestral species from which two or more descendants evolved.

---

Phylogenetic Trees

A phylogenetic tree is a hypothesis about how species are related.

flowchart TD
    A[Common Ancestor] --> B[Ancestor 1]
    A --> C[Ancestor 2]
    B --> D[Species 1]
    B --> E[Species 2]
    C --> F[Species 3]
    C --> G[Ancestor 3]
    G --> H[Species 4]
    G --> I[Species 5]

Reading a Tree

• Tips (leaves) are modern species or other taxa.
• Branches represent lineages evolving through time.
• Nodes (where branches join) represent common ancestors.
• Time usually flows from root (oldest) to tips (present).
• Branch length may represent time, number of mutations, or simply be arbitrary.

Species that share a more recent common ancestor (node) are more closely related. To see how close two species are, trace back to the first shared node; the older the node, the more distant the relationship.

What Phylogenetic Trees Are NOT

• Ladders of progress. Evolution does not "aim" at any species.
• Rankings. No species is more "advanced" than another.
• Predictions of relatedness by position. You cannot say two tips are close just because they are drawn near each other — follow the branches.

---

Building Trees: Cladistics

Modern phylogenetic trees are built using cladistics, a method that groups species by shared derived characteristics (synapomorphies). The reasoning: if two species share a feature that arose after they split from most other species, they probably inherited it from a common ancestor that none of the others had.

Character Polarity

A character can be:

• Primitive (plesiomorphic) — inherited from a distant ancestor, shared by many groups.
• Derived (apomorphic) — arose more recently in the group.

Having a backbone, for instance, is a derived feature for all vertebrates (no non-vertebrate has one), making all vertebrates a clade.

Worked Example

Consider five animals: amoeba, trout, frog, lizard, mouse. Which are most closely related?

Character	Amoeba	Trout	Frog	Lizard	Mouse
Multicellular	No	Yes	Yes	Yes	Yes
Backbone	No	Yes	Yes	Yes	Yes
Four limbs	No	No	Yes	Yes	Yes
Amniotic egg	No	No	No	Yes	Yes
Fur and milk	No	No	No	No	Yes

Each new character defines a smaller nested clade:

flowchart TD
    A[All] --> B[Amoeba]
    A --> C[Multicellular]
    C --> D[Non-vertebrate]
    C --> E[Vertebrates]
    E --> F[Trout]
    E --> G[Tetrapods]
    G --> H[Frog]
    G --> I[Amniotes]
    I --> J[Lizard]
    I --> K[Mammals/Mouse]

The tree shows that mouse and lizard are more closely related to each other than either is to frog, because they share the amniotic egg — a synapomorphy that arose in their common ancestor.

---

Molecular Phylogenetics

Cladistic analyses can use morphology, but today molecular data dominate. Molecular evidence includes:

1. DNA Sequences

The DNA sequence of a gene (or the whole genome) can be compared between species. Similar sequences suggest recent common ancestry; dissimilar sequences suggest more distant ancestry. The number of differences can even be used as a rough molecular clock to estimate how long ago two species diverged.

Commonly used genes for phylogenetics:

• Ribosomal RNA genes (e.g. 16S rRNA in prokaryotes, 18S rRNA in eukaryotes) — slow-evolving, universal, ideal for deep relationships.
• Mitochondrial DNA (mtDNA) — fast-evolving, maternally inherited, useful for recent splits within species.
• Highly conserved proteins like cytochrome c, histones and ubiquitin — ideal for comparisons across broad evolutionary distances.

2. RNA Sequences