BIO153 Lecture 6
Page 1: Introduction
University of Toronto Mississauga Arbor Lecture 6
Course: BIO153 Diversity of Organisms
Instructor: Ichiro Inamoto
Page 2: Question on Coffee Acquisition
Scenario presented:
A student arrived at UTM via public bus at 8:30 AM and was seen in IB110 at 9:05 holding a cup of coffee from Tim Horton's.
Question: What is the more likely explanation for how the student got the coffee?
Walked from the bus stop to Tim Hortons for coffee.
Took a convoluted route involving multiple coffee stops before arriving at IB110.
Page 3: Cladistics Overview
Definition of Cladistics: An approach in systematics that classifies organisms based on ancestral relationships.
Definition of Clades: Groups of organisms classified together.
Clade relationships: A clade does not necessarily reflect 'correct' evolutionary relatedness among grouped organisms.
Example Clades: Primates/Rodents, Moles/Hedgehogs, Cats/Dogs/Seals, and Horses/Rhinos.
Clade 1: Monotremes
Clade 2: Marsupials
Clade 3: Placentals
Page 4: Monophyletic Groups
Definition: A clade that includes all members as descendants of their most recent common ancestor.
Example: Clade ABC is monophyletic.
Relative reference: The classification can change based on what members are included/excluded from the clade.
Page 5: Paraphyletic Groups
Definition: A group that includes all descendants of the most recent common ancestor but excludes some.
Example: Clade DEF shares the most recent ancestor but excludes descendent G.
Characteristics: These groups are incomplete representations of close evolutionary relatives.
Page 6: Historical Misclassification
Discussion of reptiles: Birds are closely related to lizards and dinosaurs.
Historical misclassification resulted in "Reptiles" being paraphyletic by excluding birds.
Page 7: Polyphyletic Groups
Definition: A clade which includes organisms from different evolutionary lineages.
Example: Clade ABCD with mixed lineages from different ancestors.
Caution: Differences between para- and polyphyletic groupings can be debated, leading to complexity in classification.
Page 8: Classification Mistakes
Common Misclassifications:
Paraphyletic (e.g., excluding dolphins from Deer/Hippo clade)
Polyphyletic (e.g., classifying Dolphins and Seals together due to superficial similarity).
Page 9: Understanding "Algae"
Definition: Eukaryotic photoautotrophs that are not classified as plants.
Historical views incorrectly labeled many non-plant organisms as algae.
Algal species belong to multiple independent taxa, making 'Algae' a polyphyletic group.
Page 10: Cyanobacteria
Notable Mention: Cyanobacteria also referred to as 'blue-green algae', showcasing the common naming issues.
Page 11: Classification Guidelines
Cladistics Approach: Organize organisms by prioritizing ancestry.
Key Guidelines:
Track shared ancestral vs. derived characters.
Beware of traits arising from convergent evolution.
Page 12: Ingroup and Outgroup Defined
Ingroup: The species under classification (e.g., frog, cow, dog).
Outgroup: A closely related species that shares no common derived traits (e.g., fish).
Character Table Creation:
Use homologous traits to create a table reflecting presence (1) or absence (0) of traits across species.
Page 13: Phylogenetic Tree Construction
Initial Tree Building: Start by separating the outgroup from the ingroup based on traits.
Example: Fish lineage vs. Frog/Cow/Dog lineage based on the presence of four legs.
Page 14: Further Divergences
Post-Divergence Analysis: Assess which lineage evolved specific traits, such as four legs.
Traits' Evolution: Certain traits may derive only in specific lineages while remaining absent in others.
Page 15: More Divergences
Classifying Differences: Identify how the ingroup diverged into 'mammals' and 'non-mammals' based on shared ancestry.
Page 16: Final Divergences
Final Steps in Classification: Distinguishing within mammals based on traits like canines and milk feeding.
Page 17: Analyzing Evolution Conditions
Question Posed: Which traits are likely the result of evolutionary pathways?
Page 18: Maximum Parsimony Principle
Definition: The simplest explanation among multiple possibilities is often the most likely.
Application: Utilized in cladistics and further analysis regarding organisms' traits.
Page 19: Gene Classification in Cladistics
Gene Studies: Mutations in genes are analyzed separately for phylogenetic inference.
Page 20: Gene Mutation Analysis
Example with Site 1: Ancestral sequence evaluations lead to examining the most parsimonious evolutionary pathways.
Page 21: Continued Mutation Examination
Illustration of Site 4: Refining the understanding of mutation events and their evolutionary implications.
Page 22: Mapping Evolution Events
Comprehensive Scenario Mapping: Evaluate multiple evolutionary pathways to identify the most parsimonious and plausible scenarios.
Page 23: Discrepancy Resolution
Overall Mapping: Align all evolutionary events across all scenarios to determine the best explanation.
Page 24: The Role of Computers in Molecular Genetics
Computational Necessity: As species to resolve increase, the complexity of trees and calculations grows dramatically.
Maximum likelihood methods help to analyze mutation frequency in phylogenetics.
Page 25: Complexity of Taxonomy
Horizontal Gene Transfer (HGT): Challenges the traditional ancestor-descendant model, complicating lineage relationships.
Implications for classification: HGT may lead to misleading classifications regarding organism relationships.