Phylogenetic Trees

Phylogenetic Trees: A Comprehensive Study Guide

Maximizing Your Learning from Flipped Lectures

To ensure you get the most out of these flipped lectures, follow these key steps:

Prepare Your Materials: Have the slides in your preferred note-taking format readily available as the video will display them, making it easier to follow along and focus.
Active Engagement: Do not hesitate to pause the video to jot down questions or rewind to re-listen to and fully grasp a concept. There are no time limits, and thorough preparation is crucial for in-person clicker questions.
Post-Video Review: After watching, review the key terms and complete the concept check in your lecture guide to solidify your understanding for the in-class session.
Organize Questions: Compile any lingering questions you have after the lecture so you can ask them effectively during the in-person session, clarifying any points of confusion before graded clicker questions begin.

Introduction to Evolutionary Notation: Phylogenetic Trees

Evolutionary Processes: We have previously discussed microevolutionary processes and how their accumulation leads to macroevolution and speciation.
Evolutionary Notation: A critical, practical topic is evolutionary notation, which visually describes evolution.
Phylogenies/Evolutionary Trees: As observed in Lab 2, evolutionary biologists use diagrams called evolutionary trees or phylogenies to depict evolutionary relationships.
Course Relevance: Understanding how to read and interpret these trees is essential particularly as we transition to studying the 'products' of evolution.
Darwin's Pioneering Work: The only figure in Darwin's Origin of Species was the first phylogeny.
- Definition of Phylogeny: A phylogeny is a diagram illustrating relationships or how organisms are related to one another.
- Common Descent: Trees reflect Darwin's novel idea of common descent – the concept that one ancestral population can diverge into two different species, which are descended from that common ancestor.
  - Each intersection point (node) on Darwin's tree signifies an ancestral population that diverged into new species.
  - This ancestral population is the common or shared ancestor of the descendant species.
  - Common descent implies that all organisms are related and share a common ancestor.
- Transmutation of Species: Tree diagrams also illustrate Darwin's idea of transmutation of species, meaning new species arise from pre-existing species, visibly shown as one species branching into two.
Intuition in Phylogeny: Even without formal knowledge, humans intuitively recognize closer relationships (e.g., a dog and cat are more related to each other than to a maple tree) because they share a more recent common ancestor and have inherited traits from it.

Anatomy and Interpretation of Phylogenetic Trees

Tree Diagram Components:
- Tree: The entire diagram.
- Time: Always runs from the bottom (past) to the top (present).
- Branches: The diagonal lines representing genetic change. Greater distance between lines indicates more genetic difference between the organisms.
- Node: An intersection point on a branch, representing a species in the past that is the ancestor to all organisms branching away from that point.
  - A split following a node signifies a speciation event.
- Closer Relatedness Test: The ultimate test of who is more closely related is how recently they share a common ancestor (i.e., how close the shared node is to the present).
- Tips: The ends of the branches (not

Phylogenetic Trees: A Comprehensive Study Guide

Maximizing Your Learning from Flipped Lectures

To ensure you get the most out of these flipped lectures, follow these key steps:

Prepare Your Materials: Have the slides in your preferred note-taking format readily available as the video will display them, making it easier to follow along and focus.
Active Engagement: Do not hesitate to pause the video to jot down questions or rewind to re-listen to and fully grasp a concept. There are no time limits, and thorough preparation is crucial for in-person clicker questions.
Post-Video Review: After watching, review the key terms and complete the concept check in your lecture guide to solidify your understanding for the in-class session.
Organize Questions: Compile any lingering questions you have after the lecture so you can ask them effectively during the in-person session, clarifying any points of confusion before graded clicker questions begin.

Outline: Phylogenetic Trees

Introducing trees and tree terminology
- Phylogenies/Evolutionary Trees: Evolutionary biologists use diagrams called evolutionary trees or phylogenies to depict evolutionary relationships.
- Darwin's Pioneering Work: The only figure in Darwin's Origin of Species was the first phylogeny.
  - Definition of Phylogeny: A phylogeny is a diagram illustrating relationships or how organisms are related to one another.
  - Common Descent: Trees reflect Darwin's novel idea of common descent – the concept that one ancestral population can diverge into two different species, which are descended from that common ancestor.
    - Each intersection point (node) on Darwin's tree signifies an ancestral population that diverged into new species.
    - This ancestral population is the common or shared ancestor of the descendant species.
    - Common descent implies that all organisms are related and share a common ancestor.
  - Transmutation of Species: Tree diagrams also illustrate Darwin's idea of transmutation of species, meaning new species arise from pre-existing species, visibly shown as one species branching into two.
- Tree Diagram Components:
  - Tree: The entire diagram.
  - Time: Always runs from the bottom (past) to the top (present).
  - Branches: The diagonal lines representing genetic change. Greater distance between lines indicates more genetic difference between the organisms.
  - Node: An intersection point on a branch, representing a species in the past that is the ancestor to all organisms branching away from that point.
  - Taxon/Taxa: A named group of organisms (e.g., species, genus, family).
  - Clade: A group of organisms that includes a common ancestor and all of its descendants (a monophyletic group).
  - Sister taxa: Two descendant taxa that share an immediate common ancestor and are each other's closest relatives.
  - Outgroup: A taxon that is distantly related to the group of organisms being studied (the ingroup) and is used to infer the ancestral state of characters.
  - Nodes twist without affecting evolutionary relatedness: The arrangement of branches around a node can be rotated without changing the evolutionary relationships inferred by the tree.
  - Universal common ancestor (UCA): The most recent common ancestor of all current life on Earth.
  - Most recent common ancestor (MRCA): The most recent individual from which all organisms in a group are directly descended.
How to make trees from molecular data
a. Parsimony: In phylogenetics, the principle that the phylogenetic tree requiring the fewest evolutionary changes (e.g., character state transitions, mutations) to explain the observed data is the most likely or preferred hypothesis.
- Making trees with DNA data: Using genetic sequences (DNA, RNA) to infer evolutionary relationships by comparing similarities and differences.
- Do mutations in a single species give more or less information for phylogeny building than mutations in multiple species?: Mutations in multiple species provide more comparative information for determining relationships than mutations within a single species, as phylogenies inherently compare divergence between lineages.
And if you don't have molecular data?
a. Homology and homoplasy:
```
- **Homologous traits**: Traits shared by two or more species that were inherited from a common ancestor.

- **Homoplasious traits/Convergent traits**: Traits that are similar due to convergent evolution (independent evolution of similar features in species from different lineages) rather than shared ancestry.
```
- Non-DNA traits used for making phylogenies: Morphological, behavioral, physiological, or biochemical characteristics used to infer relationships when molecular data is unavailable or insufficient.
- Derived traits vs. ancestral traits:
  - Ancestral trait (Plesiomorphy): A trait inherited from a distant common ancestor.
  - Derived trait (Apomorphy): A trait that evolved in the lineage leading to a clade and that sets members of that clade apart from other lineages.
- Making trees with traits tables: Using character matrix tables (presence/absence or state of specific traits) to construct phylogenetic trees, often through parsimony methods.
Putting events on trees
- A split following a node signifies a speciation event.
- The ultimate test of who is more closely related is how recently they share a common ancestor (i.e., how close the shared node is to the present).
- Placing event "tick marks" on trees: Indicating evolutionary events like mutations, trait changes, or speciation points on the branches of a phylogeny.
Does taxonomy reflect phylogeny?
a. Monophyly and paraphyly:
```
- **Monophyletic group (Clade)**: A group consisting of a common ancestor and all of its descendants.

- **Paraphyletic group**: A group consisting of a common ancestor and some, but not all, of its descendants.
```
- Prokaryotes: A broad term for single-celled organisms that lack a membrane-bound nucleus and other membrane-bound organelles (e.g., bacteria and archaea); often considered a paraphyletic group in phylogenetic contexts.

KEY TERMS/CONCEPTS

Common descent: The concept that one ancestral population can diverge into two different species that are descended from that common ancestor, implying all organisms are related and share a common ancestor.
Common ancestor: An ancestral population represented by an intersection point (node) on a phylogenetic tree, from which descendant species diverged.
Phylogeny: A diagram illustrating relationships or how organisms are related to one another; an evolutionary tree.
How is time represented on a phylogeny?: Time always runs from the bottom (past) to the top (present).
Branches: The diagonal lines on a phylogenetic tree representing genetic change.
Nodes: An intersection point on a branch, representing a species in the past that is an ancestor to all organisms branching away from that point. A split after a node signifies a speciation event.
Tips: The ends of the branches.
Great chain of being: A hierarchical concept from ancient Greek philosophy, revived in the Medieval period, that ordered all life from the simplest to the most complex and perfect, with no evolutionary change or common ancestry.
Why is a phylogeny different than a "great chain"?: Phylogenies depict evolutionary relationships based on common descent and branching divergence, showing an interconnected web of life with change over time, whereas the "great chain" is a static, linear, hierarchical, and non-evolutionary ordering of life.
Taxon/Taxa: A named group of organisms (e.g., species, genus, family).
Clade: A monophyletic group, consisting of a common ancestor and all of its descendants.
Sister taxa: Two groups of organisms that share an immediate common ancestor not shared by any other group, making them each other's closest relatives on the tree.
Outgroup: A taxon used in a phylogenetic analysis that is known to be distantly related to the taxa under study (the ingroup) and helps to root the tree and determine ancestral character states.
Nodes twist without affecting evolutionary relatedness: The rotational equivalence of branches around a node, meaning that rotating the branches does not change the phylogenetic relationships depicted.
Making trees with DNA data: The process of using genetic sequences (nucleotide or amino acid) to infer evolutionary relationships, often relying on sequence alignment and computational models of evolution.
Parsimony: In phylogenetics, the principle that the phylogenetic tree requiring the fewest evolutionary changes (e.g., character state transitions, mutations) to explain the observed data is the most likely or preferred hypothesis.
Do mutations in a single species give more or less information for phylogeny building than mutations in multiple species?: Mutations in multiple species provide more information for phylogeny building because phylogenies illustrate the divergence and relationships between species or lineages. Mutations within a single species track variation within that species, which is less directly useful for resolving inter-species relationships.
Non-DNA traits used for making phylogenies: Observable characteristics or features of organisms, such as morphology, anatomy, development, behavior, or biochemical pathways, that are not directly encoded as DNA sequences but can be used to infer evolutionary relationships.
Homoplasious traits/Convergent traits: Similar traits that have evolved independently in different lineages, rather than being inherited from a common ancestor. This often occurs in response to similar environmental pressures.
Homologous traits: Traits in different species that are similar because they were inherited from a common ancestor.
Derived traits vs. ancestral traits:
- Ancestral trait (Plesiomorphy): A trait that was present in the common ancestor of a group.
- Derived trait (Apomorphy): A trait that evolved more recently in a specific lineage, distinguishing it from older ancestral traits or other lineages.
- Synapomorphy: A shared derived trait, which is particularly useful for defining clades.
Making trees with traits tables: The method of constructing phylogenetic trees by organizing discrete character states (traits) of different taxa into a data matrix, then using algorithms (like parsimony) to find the tree that minimizes evolutionary changes.
Placing event "tick marks" on trees: Annotating phylogenetic trees with specific evolutionary events such as gain or loss of traits, speciation events, or major genetic mutations, denoted by markers on branches.
Universal common ancestor (UCA): The single organism or population that is the most recent common ancestor of all life on Earth.
Most recent common ancestor (MRCA): The most recent individual from which all organisms in a defined group are directly descended.
Monophyletic: A group (clade) that includes a common ancestor and all of its descendants.
Prokaryotes: Single-celled organisms that lack a membrane-bound nucleus and other membrane-bound organelles (Bacteria and Archaea). Phylogenetically, the term "prokaryote" often refers to a paraphyletic group because it excludes eukaryotes, which are descendants of some prokaryotic ancestors.
Paraphyletic: A group that includes a common ancestor but not all of its descendants.
Why are birds dinosaurs? Are they still birds?: In the context of phylogeny, birds (avian dinosaurs) are considered the direct descendants of a group of feathered, non-avian dinosaurs (specifically, maniraptoran theropods). Therefore, cladistically, birds are dinosaurs, as they form a monophyletic group that includes all descendants of their most recent common ancestor, which was a dinosaur. Yes, they are still considered birds because "birds" is a subgroup within the larger dinosaur clade.
Why doesn't taxonomy always reflect phylogeny?: Traditional taxonomy, especially older classification systems, sometimes group organisms based on overall similarity or common traits that might not accurately reflect their evolutionary history. This can lead to the creation of paraphyletic or polyphyletic groups (groups that don't include all descendants of a common ancestor, or groups whose members don't share an immediate common ancestor, respectively). For taxonomy to perfectly reflect phylogeny, all taxonomic groups should ideally be monophyletic (clades).