Phylogenetic Analysis and Tools

Phylogenies and Their Uses

• Phylogenies reconstruct the history of life.
• Phylogenies are often useful for understanding organisms.
• They can be helpful for identifying evolutionary patterns.
• They help determine which traits are older or younger.
• Phylogenies show relationships between traits and evolutionary changes.
• Traits related to ecology and lifestyle can be assessed through phylogenies.
• Biological properties of ancestors can be determined.

Phylogenetic Approaches and Tools

• The Tree of Life Web Project (ToL) is a project for biologists to explore the diversity of organisms and their evolutionary history.
• The ToL project uses a hierarchical structure of evolutionary trees to illustrate the genetic links between living organisms.

Basic Units of Phylogenetic Analysis

• Taxa range from individuals to higher taxonomic levels (e.g., genera, phyla).
• Characters are measurable attributes, from DNA sequences to complex traits.
• Character states are distinct forms of a character (e.g., "G" or "A").

Phylogenetic Methods

• Phenetics is a distance-based method for inferring relationships based on similarities between organisms.
• Cladistics reconstructs branching patterns using shared derived character states (synapomorphies). Shared derived characteristics are crucial for determining evolutionary relationships.
• Shared derived characters illustrate evolutionary relationships. Traits are often inherited through a common ancestor.
• The outgroup method uses an outgroup to determine ancestral states in a phylogeny.
• The outgroup method can be important when phylogenetic history is not well understood.

Determining Character State Polarity

• Outgroup method (most common method) needs knowledge of phylogenies.
• Identifying the ancestral state in a phylogeny assumes the outgroup state represents the ancestral state.
• Different outgroups may provide conflicting inferences about ancestral states.

Fossil Record and Developmental Biology

• Fossils can be used to determine ancestral states if the fossil record is relatively complete.
• Incomplete fossil records may lead to erroneous inferences about ancestral states.
• Developmental biology can be used to infer ancestral and derived states. Derived traits may appear later in the developmental stage of an organism.

Methods of Phylogenetic Inference

• Maximum likelihood methods evaluate probabilities that data is observed given a model and phylogeny.
• Bayesian methods use probabilities based on models of evolutionary history and assumptions about tree and parameter distributions.

Difficulties in Phylogenetic Inference

• Rapid radiations (like with the Hawaiian silversword alliance) complicate phylogenetic inference.
• The fossil record, which is often incomplete, can result in difficult phylogenies.
• Incomplete lineage sorting (ILS) can cause misinterpretations of relationships in recent populations.
• Short internal branches can complicate the analysis of relationships between species.

Phylogenetic Analysis of Life

• Evolutionary history is illustrated through phylogenies.
• Evolution can be tracked using the fossil record, as well as by analyzing shared traits.
• Molecular data can help determine how quickly species evolved.

Additional Notes

• Shared ancestral traits (plesiomorphies) should be distinguished from derived traits (apomorphies) when determining evolutionary relationships. If ancestral traits are used, it might not show the true evolutionary path.
• The comparative method investigates general evolutionary patterns and correlations between traits and time.
• Testes size and body mass are correlated with mating systems, indicating the importance of the environment on the evolution of these traits.