Phylogeny and the Tree of Life Study Notes

Phylogeny and the Tree of Life

  • Lecture by John Cozza, FIU Biology Department.
  • Adapted Material: Some contents from BIS 2C, UC Davis.
  • Copyright © JC & FIU.
  • Lecture Information: Cannot share, post or sell.
  • Relevant Reading: Openstax chapter 20, Campbell chapter 20, Tree of Life Web Project (http://tolweb.org/tree/learn/concepts/whatisphylogeny.html)

Schedule Overview

  • Week 1
    • Monday Jan 5
    • Introductory Course: John C. & Vicenta S.
      • Action: Read syllabus
    • Wednesday Jan 7
    • Topic: Phylogeny
    • Campbell: Chapter 20
    • Openstax: Chapter 20
    • Friday Jan 9
    • Topic: Phylogeny Continued
    • Week 2
    • Monday Jan 12: Phylogeny
    • Tuesday Jan 13: Reference Khan (2017)
    • Wednesday Jan 14: The Origin and Diversity of Life (Campbell 24.1)
    • Friday Jan 16: Viruses/Prokaryotes
    • Monday Jan 19: Martin Luther King Day (Holiday)
    • Wednesday Jan 21: Prokaryotes (1st participation with LAS!)
    • Friday Jan 23: Photosynthesis
    • Monday Jan 26: Protists (Preparation)
    • Wednesday Jan 28: Plant Evolution
    • Friday Jan 30: Plant Diversity
    • Monday Feb 2: Exam 1 - Phylogeny & Microbes (based on lectures and readings)

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Weekly Objectives

  • Check Canvas for course introduction presentations.
  • Read syllabus thoroughly and raise queries.
  • Confirm existence of exam conflicts.
  • Watch Dr. Chew's videos for study strategies.
  • Obtain and register iClicker device.

Office Hours Details

  • Open office hours available in OE 216:
    • Wednesdays 3-5 PM
    • Thursdays 4-5 PM (extratime if needed)
    • Fridays 3-5 PM
  • Email for quick queries: jcozza@fiu.edu (not through Canvas).

Distractions Management

  • Recommendations for optimal learning:
    • Turn off phones and minimize distractions.
    • Use laptops exclusively for biology content.

Understanding Phylogeny

Main Outline

  • Phylogeny unfolds as a tree of life showing relationships among species.
  • Concept of reconstructing phylogenetic trees involves understanding:
    • Shared ancestry
    • Interpretation of evolutionary relationships.

What is the Tree of Life?

  • Representations of unity of life encompassing all biological diversity.
  • Examples from cultures include:
    • Mayan World Tree
    • Celtic Tree of Life
  • Emphasis on interconnectedness and evolution.

Phylogenetic Trees as Simplifications

  • Trees simplify complexity of life forms.
  • Represent evolutionary lineage rather than a straightforward chronological timeline.

Components of Phylogenetic Trees:

  1. Branch Points: Represent split of phylogenetic lineages.
  2. Sister Taxa: Closely related taxa that share a recent common ancestor.
  3. Clades: A group consisting of an ancestor and all its descendants; can be monophyletic, paraphyletic, or polyphyletic.
  4. Ancestral vs. Derived Traits:
    • Ancestral: Traits present in a common ancestor.
    • Derived: Traits that have changed from the ancestor.
  5. Homology vs. Homoplasy: Homologous traits are inherited from a common ancestor; homoplastic traits arise independently in different lineages.
  6. Outgroup/Ingroup Comparison: Outgroup provides a reference for identifying ancestral vs. derived characteristics.

Methods of Phylogenetic Reconstruction

  • Homology: Focus on shared traits for comparison.
  • Parsimony: The principle of preferring the simplest explanation with the least changes.
  • Maximum Likelihood: A statistical method that evaluates the probability of the data under various possible tree topologies based on specific models.

Types of Trees

  • Cladogram: Only branching patterns shown.
  • Chronogram: Time-scaled representation of phylogenetic relationships.
  • Phylogram: Represents branch lengths as proportional to evolutionary change.

Practice Definitions

  • Key terms for understanding phylogenetic principles:
    • Clade: Most recent common ancestor and all its descendants.
    • MRCA (Most Recent Common Ancestor): The last ancestor shared between two lineages.
    • Synapomorphy: A shared, derived trait that defines a clade.
    • Outgroup: A taxon outside the clade being studied, useful for grounding the analysis.

Phylogenetic Examples

  • Human Phylogeny: Detailed connections between human ancestors and various primate species.
  • Note traits shared with ancestors, such as bipedalism or brain size developments in various Homo species, indicating evolutionary adaptation.

Disease Evolution Research

  • Investigations into the phylogenetic relationships of HIV and SIV illustrate co-evolution between viruses and hosts, aiding in understanding pandemic dynamics.
  • Use of trees to depict origin and transmission pathways.

Biodiversity Study Significance

  • Understanding phylogeny dives into the immense diversity of life that underpins ecological balance.
  • Enables predictions about future biodiversity in changing environments and impacts of human activity.