Mod5 Feb12 Phylogeny-Tree of Life_for students (1)

Page 1: Introduction to Phylogeny

• Date: February 12, 2025

• Topic: Phylogeny and the Tree of Life

• Key Example: Heliconius butterfly phylogeny

• Important Reminders:

  • Homework 5 due: February 21

  • Discussion: Test review and grading updates

• Concept:

  • A phylogenetic tree represents the evolutionary relationships among species.

  • Phylogeny: The evolutionary history of a species or group of species.

Page 2: Learning Objectives

• Objective 5: The evolutionary relationships among species, genes, populations, and higher order taxa can be depicted using phylogenetic trees.

Page 3: Learning Outcomes

• Outcomes include:

  • Interpreting phylogenetic trees to identify key elements (e.g., out-group, nodes, common ancestors, sister taxa, monophyletic groups).

  • Using phylogenetic trees to support or reject hypotheses (e.g., relationship between birds and dinosaurs).

  • Exploring evolutionary relationships through various data types (morphology, developmental patterns, nucleotide sequences).

  • Examples of convergent and divergent evolution between species and comparison of homologous and analogous traits.

Page 4: Importance of Studying Phylogeny

• Classification: Organizes diversity of life using accurate relatedness patterns.

• Forensics: Assesses DNA evidence in legal cases to determine relationships (e.g., criminal investigations).

• Pathogen Origins: Identifies and relates species involved in new pathogen outbreaks.

• Conservation: Informs policies to protect endangered species.

• Bioinformatics: Integrates computing algorithms with biology to analyze molecular data and create optimal phylogenetic trees.

Page 5: Outline of Key Topics

• Introduction

• Hierarchical classifications

• Key features of a phylogeny

• Interpreting a phylogeny

• Practice: Using a phylogeny

Page 6: Understanding Macroevolution

• Macroevolution: Evolution on a scale larger than species speciation.

• Phylogeny: Hypothesized evolutionary relationships depicted in a phylogenetic tree.

• General Principles:

  • All organisms relate to each other through descent from a common ancestor.

  • Evolution follows a bifurcating pattern indicating speciation.

  • Lineages change characteristics over time.

Page 7: Darwin’s Concept of Evolution

• Quote from Darwin: "As buds give rise by growth to fresh buds..."

  • Represents the interconnectedness of life through evolutionary branches.

  • Core Idea: Species undergo change and descend from ancestral species through modification.

Page 8: Evolutionary Tree Visualization

• Tree of Life: Visual representation of evolutionary relationships (rooted, branching tree).

• Example: Evolutionary lineage of primates including Rhesus monkeys, baboons, orangutans, chimpanzees, and humans.

Page 9: Diversity in Life Forms

• Illustrated Tree of Life showing various bacterial groups and major domains:

  • Bacteria, Archaea, Eukarya, with numerous phyla highlighted.

Page 10: Taxonomy Basics

• Taxonomy: Science of classifying and naming organisms.

• Developed by Carolus Linnaeus focusing on morphological characteristics.

• Two-part names known as binomial nomenclature examples:

  • Panthera pardus (leopard)

• Hierarchical classification system:

  • Genus: Panthera

  • Family: Felidae

  • Order: Carnivora

  • Class: Mammalia

  • Phylum: Chordata

Page 12: Hierarchical Classification Explained

• System for grouping species into inclusive categories.

• Definition of taxon: A taxonomic unit at any hierarchy level.

• Mnemonic: "Kings Play Chess On Fine Green Silk" representing classification hierarchy.

Page 13: Systematics versus Linnaean Taxonomy

• Evolutionary relationships often differ from traditional Linnaean taxonomy.

• Systematics: Classifies organisms and determines evolutionary relationships, represented in phylogenies.

Page 14: Differences in Classification

• Example:

  • Taxonomy: Class Aves (birds), Class Reptilia (reptiles)

  • Systematics: Birds are included in the reptile clade based on evolutionary relationships.

Page 16: Features of Phylogenetic Trees

• Key components of a phylogenetic tree:

  • Taxon: Each species or unit on the tree.

  • Sister taxa: Groups sharing the most recent common ancestor.

  • Time line indicating evolutionary sequence.

Page 17: Understanding Branch Points

• Branch Point: Represents divergence between lineages (common ancestors).

  • Example: Illustration with taxa A-G showing relationships.

  • Distinction between rooted and unresolved branches.

Page 18: Rotating Branches in Phylogenies

• Visualization that shows rotation of branches does not affect evolutionary relationships depicted in the phylogenetic tree.

• Human-Chimpanzee relationship remains unchanged despite branch rotation.

Page 19: Understanding Different Tree Representations

• Explanation of how tree branches can be rotated.

  • All trees represent the same evolutionary history despite appearance differences.

Page 20: Identical Phylogenies

• Example showing two trees are identical, outlining the relationship between humans and chimpanzees as sharing the closest common ancestor.

Page 21: Clades and Monophyletic Groups

• Clades: Groups that include a common ancestor and all its descendants (living or extinct).

• Monophyletic groups key to evolutionary classification.

Page 22: Definition and Characteristics of Clades

• Explanation that clades can contain larger clades.

• Hierarchical nature of clades in the tree of life.

Page 23: Analyzing Phylogenetic Trees

• Questions posed regarding which trees depict the same evolutionary history.

Page 24: Identifying Monophyletic Groups

• Task to determine which shaded groupings are monophyletic examples.

Page 25: Structure of Outline

• Reiterate the outline for section organization: Introduction, Hierarchical classifications, Key features of phylogeny, Interpreting phylogeny, and Practice exercises.

Page 26: Reconstructing Phylogenies

• Learning Objective: To infer phylogenies using data concerning morphology, development, behavior, and molecular sequences.

• Homologies as indications of shared ancestry versus convergent evolution leading to analogous structures.

Page 27: Homologous Structures

• Definition: Anatomical resemblances with variations based on common ancestral traits.

  • Examples include human, cat, whale, bat forelimbs showing homologous structures.

Page 28: Convergent Evolution

• Analogous Structures: Similar in function, arise independently in different lineages due to similar selective pressures.

• Example: Similarities in lizard traits without common ancestry due to evolution driven by similar environments.

Page 29: Further Convergent Evolution Examples

• Compares bat and bird wings showing homologous bones from a common ancestor.

• Highlights distinction between converging and homologous traits.

Page 30: Identifying Examples of Convergent Evolution

• Query questioning examples of convergent evolution and its characteristics.

Page 31: Homologous Structures During Development

• Notable that homologies can be embryonic rather than observable in adult forms (e.g., human and chick embryos).

Page 32: Vestigial Structures as Evidence

• Vestigial Structures: Historical remnants of functionality in ancestors,

  • Examples: Appendix, tailbone, wisdom teeth, functionless eyelid.

Page 33: Continued Evidence in Development

• Mention of trait remnants indicating convergences in modern species related to their ancestors.

Page 34: Phylogenetic Trees and Shared Characters

• Shared Derived Characters: Unique to specific clades, serve to build phylogenies.

• Shared Ancestral Characters: Not useful for deducing relationships within the clade (e.g., backbone).

Page 35: Utility of Outgroups

• Outgroup: Group closely related to the ingroup, allowing differentiation between ancestral and derived traits.

• Importance in aiding analysis of phylogenetic trees.

Page 36: Reiterating the Structure

• Continuation of the outline for organized presentation.

Page 37: Phylogenetic Tree Construction Skills

• Skill development in constructing phylogenetic trees based on trait tables defined:

  • Traits from ancestor vs. derived traits analysis.

Page 38: Trait Analysis in Phylogeny

• Inquiry to determine which species reflect no derived traits.

Page 39: Review of Trait Distribution

• Follow-up on trait distribution in species as reflected in evolutionary branches.

Page 40: Identifying Traits in Evolution

• Task to explore traits existing earliest in discussed species timeline.

Page 41: Shared Derived Traits for Sister Species

• Relationship between shared sister species and specific derived traits.

Page 42: Reflection on Traits in Phylogeny

• Review of specific traits delineating shared characteristics within sister species.