Phylogeny and Cladistics: Lecture 1

Course Introduction and Structure

Course Overview

This course, "Biology 2: Biological Diversity, Function, and Interaction," is divided into two parts, each with its own instructor and term test. The course covers a wide range of topics in biological diversity and evolutionary relationships, with a focus on plants and animals. Students are expected to engage with lectures, group discussions, and iClicker questions, and are responsible for both assigned readings and lecture material.

• Required Textbook: Campbell Biology (4th Canadian Edition) by Reese et al. (2020)

• Communication: Slack for content questions and announcements; email for official matters only

• Lab Information: Lab-related questions should be directed to lab instructors or TAs

Topic 1: Phylogeny & Cladistics

Introduction to Phylogeny and Systematics

Phylogeny is the study of the evolutionary history and relationships among species. Systematics is the broader discipline that includes phylogenetics (the study of evolutionary relationships), cladistics (the method of identifying clades or monophyletic groups), and taxonomy (the naming and organizing of species).

• Systematics: The scientific study of the diversity and relationships among organisms

• Phylogenetics: The study of evolutionary relationships and the construction of phylogenies

• Cladistics: A method for classifying organisms based on common ancestry

• Taxonomy: The discipline of naming and classifying organisms

What is a Phylogeny?

A phylogeny is a hypothesis about the evolutionary history of species or lineages. These hypotheses are constructed using multiple lines of evidence:

• Homologous morphology: Similar structures due to shared ancestry

• The fossil record: Provides chronological evidence of evolutionary changes

• Behaviour and habitat: Ecological and behavioral traits

• Molecular sequences: DNA and protein sequence comparisons

Phylogenetic Trees

Phylogenetic trees are diagrams that represent evolutionary relationships among species. They can be constructed for closely related species or for all known life forms. The orientation and branch lengths of these trees can vary:

• Cladograms: Show relationships; branch lengths are arbitrary

• Phylograms: Branch lengths often represent time or genetic change

Linnaean Classification and Binomial Nomenclature

The Linnaean system classifies organisms into hierarchical groups (Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species). Binomial nomenclature uses two names (genus and species) to uniquely identify organisms, reducing ambiguity.

• Example: Brassica rapa (turnip)

• Note: There is a movement to include Indigenous names in scientific nomenclature

Monophyletic, Paraphyletic, and Polyphyletic Groups

Phylogenetic trees help classify organisms into groups based on common ancestry:

• Monophyletic group (Clade): Includes an ancestor and all its descendants

• Paraphyletic group: Includes an ancestor and some, but not all, descendants

• Polyphyletic group: Does not include the most recent common ancestor of all members

Building Phylogenetic Trees

Constructing phylogenetic trees involves identifying differences among species, sorting these differences to find the simplest explanation (Occam's razor), and drawing the tree that best represents these relationships. Molecular data, such as DNA sequences, are often used to infer relationships.

• Occam's razor: The simplest explanation is preferred

• Gene sequence comparison: Used to determine relatedness among species

Example Table: Types of Phylogenetic Groups

Group Type	Definition	Example
Monophyletic	Ancestor and all descendants	Mammals
Paraphyletic	Ancestor and some descendants	Reptiles (excluding birds)
Polyphyletic	Unrelated organisms from different ancestors	Marine mammals

Applications and Importance

Understanding phylogeny is essential for classifying organisms, studying evolutionary processes, and tracing the history of life on Earth. It also informs fields such as conservation biology, ecology, and genomics.

Additional Resources and Announcements

• EDIA Resources: Equity, Diversity, Inclusion, and Accessibility contacts and support

• Volunteer Notetaking: Opportunities to support peers and contribute to an inclusive learning environment

• Emergency Procedures: Fire and power outage protocols

Additional info: Students are encouraged to review the "Research Method" in Figure 26.12 of the textbook before starting lab work. The course emphasizes the importance of both lecture and textbook material for exam preparation.