BIOS 3300 CH 4 LEC
Page 1: Review Quizzes
Review quizzes are designed to test understanding of previously covered material.
Page 2: Example - Pesticide Decision Making
Scenario: Deciding on the safety of a pesticide that effectively kills crop-eating insects.
Hypothesis: "The pesticide is dangerous to humans."
Suggested Action: The pesticide should not be used.
Consequences of Over-Credulity:
If too gullible, accept hypothesis as truth and refrain from using the pesticide.
Consequence: Crops are damaged or destroyed by pests.
Page 3: Evaluating Pesticide Risks
Probable Hypothesis: "Pesticide X is dangerous to humans."
Mistake Analysis:
Too Credulous:
Accept hypothesis as true.
Consequences include losing crops to pests.
Too Skeptical:
Reject hypothesis despite evidence.
Consequences can include human illness or fatalities.
Evaluation of Mistakes: Reflect on which mistake is worse.
Required Evidence: Discuss how much evidence is necessary before approving pesticide use.
Page 4: Estimating Evolutionary Trees
Course: BIOS 3300
Historical Note: Darwin sketched the first evolutionary tree in 1837.
Page 5: Outline of Topics
Phylogenetic Inference Logic
Evaluating Phylogenetic Trees
Questions Addressed with Phylogenies
Page 6: Key Definitions
Phylogeny: Hypothesis about evolutionary relationships among organisms.
Systematics: Process of constructing phylogenetic hypotheses.
Taxonomy: Identification and naming of species.
Organizes species into related groups.
Taxa: Taxonomic units used in classification.
Page 7: Identifying Synapomorphies
Synapomorphies: Traits shared due to common ancestry.
Derived Traits: Must understand evolutionary change direction (polarity).
Outgroup Analysis: Identifies evolutionary shifts across groups.
Important distinction: All synapomorphies are homologies, not vice versa.
Page 8: Synapomorphies Example
Four Limbs: Not a unique synapomorphy for all mammals.
Hair: Confirmed as a true synapomorphy for mammals.
Page 9: Phylogenetic Tree Reconstruction
Data Collection: Requires heritable traits for comparison.
Types of data include morphology, genetics, and behavior.
Modern Approach: Predominantly relies on molecular phylogeny using DNA data.
Page 10: Phylogenetic Hypotheses for Whales
Comparison of evolutionary relationships among different species (cows, deer, hippos, etc.)
Assessing interrelations based on shared ancestry.
Page 11: Parsimony Analysis
Understanding sequence data and its role in establishing phylogenetic relationships.
Page 12: Homoplasy Issue
Convergence and Reversal: Both are forms of homoplasy and introduce data noise.
Susceptibility of Sequence Data: More prone to homoplasy than morphological data.
Page 13: Phylogenetic Construction Methods
Maximum Parsimony: Best tree minimizes evolutionary changes.
Maximum Likelihood: Utilizes statistical models to predict amino acid changes in DNA sequences.
Page 14: Parsimony Assessment
Decision-making process to determine the best-fitting phylogenetic tree based on trait analysis.
Page 15: Tree Selection
Choose among multiple tree options based on evolutionary traits and their changes.
Page 16: Maximum Likelihood Benefits
Capable of considering various rates of evolutionary change across codons.
Page 17: Searching Possible Phylogenetic Trees
The vast potential tree configurations can complicate searches due to computational limitations.
Search Methods:
Exhaustive methods
Branch and bound techniques.
Page 18: Evaluating Phylogenetic Trees
Assessing tree effectiveness through bootstrapping.
Bootstrapping: Creates resampled datasets to estimate phylogeny.
Determines branch reliability based on iterations.
Page 19: Tree Reconstruction Basics
Rooting the Tree: Understand relative relationships before establishing the tree.
Page 20: Uses of Phylogenetic Trees
Applications in diverse areas like evolutionary biology and classification.
Page 21: Identifying Homologous Traits
Importance of clarity in trait identification and understanding its evolutionary background.
Page 22: Distinguishing Homology and Analogy
Illustrates complex relationships and shared traits among species.
Page 23: Biological Classification Principles
Taxonomists emphasize monophyletic taxa as the only valid evolutionary representation.
Page 24: Vertebrate Evolutionary Relationships
Examines classifications among groups (birds, reptiles, mammals).
Page 25: Coevolution and Speciation
Coevolution: Joint adaptation of interacting species.
Cospeciation: Parallel speciation events.
Page 26: Lactose Tolerance Evolution
Examines instances of lactose tolerance adaptations across populations.
Page 27: Applications of Phylogenetic Analysis
Utilized in health (vaccines and cancer studies) and evolutionary research (virus evolution).
Page 28: Reference
Source: Gómez-Carballa et al. on COVID-19 variant emergence.
Page 29: Review Quiz Reminder
Action: TAKE REVIEW QUIZ #3 on Evolutionary Trees.
Page 30: Discussion Notes
Discussion Theme: TREE THINKING.
Preparation Instruction: Read assigned article before class and participate in group quizzes.