Phylogeny and Tree Thinking

Explain how a phylogenetic tree represents a hypothesis about evolutionary history.

A phylogenetic tree is a diagram that represents a hypothesis about evolutionary relationships among different organisms through different characteristics such as branch points which represents common ancestors of lineages, evolutionary lineages which represent the path from the common ancestor to the descendant taxa, and sister taxa which are groups that share a unique common ancestor.

Explain how both phylogenetic trees and Linnean hierarchy group species by relatedness. Mastery level: Can a phylogenetic tree differ from Linnean hierarchy? Are all Linnean groupings monophyletic?

Phylogenetic trees depict relationships as branching diagrams and have grouping which are based on shared derived characters —> forming clades that include an ancestor and its descendants.

Linnean system classifies species into broad categories such as genus, family, and order based on morphological similarities that don’t represent evolutionary relationships..

Monophyletic: a group that includes all common ancestors and their descendants.

Describe how the nodes on a phylogeny indicate most recent common ancestors, and how branching points relate to speciation. Specifically, how do the branching points on a tree relate to the biological species concept?

Nodes on a phylogenetic tree represent the most common ancestor of the descendant lineages. Each node represents a divergence event which is when 1 lineage split into two or more distinct groups.

A branching point is when a single ancestral species diverged into two plus species. Branching point correspond to speciation events where populations evolve to become distinct species. The biological species concept represents species as groups of interbreeding populations that are isolated from other groups and so creates species which is the connection to the branching points.

Distinguish homology vs. analogy and related concepts (convergence,homoplasy)

Homology is similarities due to shared ancestry. Analogy is similarities due to convergent evolution, not shared ancestry. In other words, homology is shared embryonic origin and analogy is shared function.

Convergent Evolution: when different species independently evolve similar traits due to similar environmental pressures.

Homoplasy: a broader term that includes convergent evolution and other forms of similarity that are not due to common ancestry.

The more complex the structure, the more homologous it likely is.

Describe how homologies are used to generate phylogenetic trees. Explain how this relates to the principle of parsimony.

Homologies are used to generate similar physical structures, embryonic developmental patterns, and DNA sequences.

Phylogenetic traits are built using shared derived traits that evolved in a common ancestor and are unique to a particular clade.

The principle of parsimony states that the simplest explanation with the fewest evolutionary changes is most likely correct. In phylogenetic trees, the most parsimonious tree is the one that requires the fewest evolutionary events.

Given a phylogenetic tree, be able to:

• Find the most recent common ancestor of a set of taxa

• Determine which taxa are more closely related

• Identify the outgroup/basal taxon (if shown)

• Recognize monophyletic groups (aka clades or ‘natural groups’),

paraphyletic groups, and polyphyletic groups

• Find any polytomies and explain what they mean with respect to taxon

relatedness

• If the tree also shows evolutionary events (tick marks showing new traits,

e.g. ‘amniotic egg’), be able to describe the characteristics of a given tip or

node

• If the tree also shows evolutionary events, be able to identify examples of

convergent evolution

• look for the node where 2+ taxa connect. The closer the node is to the taxa, the more recently the taxa shared a common ancestor.

• Taxa that share a more recent MRCA are more closely related.

• The outgroup is the taxon that diverged earliest and does not share many derived traits with the rest of the group.

  • This help roots the tree

• Monophyletic groups: include an ancestor and all its descendants.

• Paraphyletic groups: include an ancestor but not all descendants.

• Polyphyletic groups: include taxa without their common ancestor.

• Polytomy: node with 3+ branches instead of a clear 2+ split

  • represents uncertainty about the exact evolutionary relationship among taxa

• Any taxon above a given tick mark inherits that trait while those below do not.

• Convergent evolution occurs when unrelated taxa evolve similar traits independently due to similar environmental pressures

  • shown by the same trait appearing on separate branches that don’t share a common ancestor

Explain why it is important to use many characters when building a phylogenetic tree. Give at least 2 reasons. Hint: one reason relates to convergence/homoplasy.

1. It reduces the impact of convergence/homoplasy when different species independently evolve similar traits due to similar environmental pressures and not shared ancestry

2. It increases accuracy and robustness as it provides a more comprehensive dataset

Mastery: How are mutation rates and fossil ages important for calibrating a molecular clock? What are some assumptions used when applying a molecular clock. Mastery level: What might happen if one or more of these assumptions are violated? How would that affect our interpretations of branching patterns (topology)? branch lengths?

Mutation Rates are crucial for calibrating molecular clock because they help estimate the rate at which genetic changes occur over time.

The fossil age provides a timeline for when certain species existed. With this, they can calibrate molecular clocks to ensure they reflect accurate evolutionary timelines.

The primary assumption is that mutations occur at a constant rate of time, but it is also assumed that mutations are neutral and don’t affect an organism’s fitness. If mutations rates are not constant, the inferred relationship between species may not be correct which could lead to incorrect estimates of the time between divergence events. This would lead to inaccurate tree topology.