1.7 Phylogenetic trees and tree thinking

In a phylogenetic tree, what are the branches, nodes, root, and tips, and what does each represent?

- Branches (vertical lines) represent lineages through time.

- Nodes are divergence points where lineages split, indicating speciation events.

- The root (trunk or base) represents the most recent common ancestor of all taxa shown.

- Tips are the endpoints representing current taxa or observed entities (e.g., species or extinct lineages).

What defines a monophyletic group, and how does it contrast with paraphyletic and polyphyletic groups? What are nested monophyletic groups?

- A monophyletic group (or clade) includes a common ancestor and all of its descendants.

- A paraphyletic group includes the common ancestor but not all descendants.

- A polyphyletic group does not include the common ancestor, grouping taxa based on similarity rather than ancestry.

- Nested monophyletic groups occur when clades are contained within larger clades (e.g., Mammalia within Amniota).

What is a synapomorphy, and how does it help identify monophyletic groups?

A synapomorphy is a shared, derived trait inherited from the most recent common ancestor of a group. It helps define and support a monophyletic group, because all members share that derived character.

How do you use the most recent common ancestor (MRCA) of two taxa on a phylogenetic tree to evaluate their relatedness?

Identify the two taxa of interest and trace backward down the branches to the MRCA (a node). Taxa sharing a more recent MRCA are more closely related than those whose MRCA is deeper (older) on the tree.

What data types are used to build phylogenetic trees, and how are they used in the construction process?

- Morphological data, such as structural features and skeletal traits.

- Genetic data, including mitochondrial DNA sequences, ribosomal RNA genes, and various genomic genes.

- These data help infer evolutionary relationships, typically using the principle of parsimony, which favors the tree requiring the fewest trait changes.