Phylogenetic Trees and Evolutionary Relationships

Patterns of Evolution

Evolution produces nested patterns of similarity in extant species and historical patterns in the fossil record.

Phylogeny and Phylogenetic Trees

Phylogeny is the history of descent with branching caused by divergence, often illustrated using phylogenetic trees. Phylogenetic trees represent patterns of common ancestry. Branches represent diverging populations or species, and tips represent the most recent time in the tree. Nodes represent common ancestors.

Interpreting Phylogenetic Trees

Phylogenetic trees are graphical hypotheses about evolutionary relationships. The closeness of relationships is determined by how recently two groups shared a common ancestor. Sister groups are two groups that are each other's closest relatives. Nodes can be rotated without changing the evolutionary relationships.

Taxon and Groups of Taxa

A taxon is a single group, while taxa are multiple groups. Important terms for describing groups of taxa include:

• Monophyletic Group (Clade): Includes a common ancestor and all its descendants; requires only one cut to remove from the tree.
• Paraphyletic Group: Includes a common ancestor and some, but not all, of its descendants; requires more than one cut to remove.
• Polyphyletic Group: Does not include the common ancestor of the taxa under consideration; also requires multiple cuts to remove; often share traits evolved independently via convergent evolution.

Only monophyletic groups reflect evolutionary relationships.

Taxonomic Classification

Taxonomic classification reflects the order of branching in phylogenetic hypotheses. Organisms are classified into domain, kingdom, phylum, class, order, family, genus, and species. Domains include eukarya, bacteria, and archaea.

Constructing Phylogenetic Trees

Phylogenetic trees are constructed by comparing anatomical, physiological, or molecular features (characters) of organisms. Different forms of a character are called character states. Similarities can be due to:

• Homology: Similarity due to common descent.
• Analogy: Similarity due to convergent evolution.

Only homologies are useful in constructing phylogenetic trees. Shared derived characters (synapomorphies) are homologies shared by some but not all members of the group.

Cladistics and Parsimony

Cladistics builds phylogenetic trees based on synapomorphies. The principle of parsimony suggests that the best-fit tree is the one with the fewest number of changes.

Molecular Data

Molecular data, such as DNA or RNA sequences, can be used to construct phylogenies through:

• Synapomorphic Method: Identifies derived ancestral molecular characters by comparing in-group data to an outgroup.
• Distance Method: Based on overall similarities; assumes that descendants of a recent common ancestor have had little time to evolve differences. The level of similarity or distance indicates how recent the last shared common ancestor of two groups was

Applications of Phylogenetic Trees

Phylogenetic placement can reveal evolutionary history and has practical uses, such as in identifying the correct classification of organisms and tracing the spread of diseases.