Evolutionary Theory and Phylogenetics Lecture Notes Review

Descent with Modification and Natural Selection

Descent with Modification

• Definition: The fundamental idea proposed by Darwin, suggesting that all life shares a common ancestor and has diversified over vast expanses of time.
• Evidence Categories:
  • Age of Earth:
    • Radiometric dating confirms the immense age of Earth, providing the necessary timeframe for evolutionary change.
    • The Geologic Time Scale quantifies this history.
  • Change through Time: Species are not immutable but rather mutable.
    • Selective Breeding: Artificial selection by humans demonstrates that species can change drastically over generations (e.g., dog breeds from wolves).
    • Direct Observation: Evolutionary changes can be observed within human lifetimes.
      • Example: The development of resistance to antiviral drugs like AZT in HIV populations, moving from susceptible to partially resistant to highly resistant forms within a short period.
    • Vestigial Traits: Reduced or rudimentary structures with no current function, serving as remnants of ancestral features.
      • Often referred to as inherited "junk" DNA.
      • Pseudogenes: Non-functional relatives of genes that have lost their ability to code for functional proteins or are no longer expressed in the cell.
  • New Species Arise, Newer Forms Derive from Older: This indicates a branching pattern of evolution.
    • Fossil Record: Provides a chronological sequence of organisms, showing changes over time.
    • Transitional Forms: Fossils that exhibit characteristics of both an ancestral group and its descendant group, bridging evolutionary gaps.
      • Example: Sinosauropteryx and Archaeopteryx illustrate transitions between theropod dinosaurs and birds.
      • These forms represent a series of intermediate steps in evolution, rather than a single "missing link."
    • Biogeography: The study of the geographical distribution of species.
      • Law of Succession: Fossil and living organisms in the same geographic region are related to each other but are distinctly different from organisms found in other areas.
      • Example: The extinct glyptodont, an armored mammal, is closely related to the extant armadillo, both found in the Americas.
  • Common Ancestry: All life shares a common origin.
    • Homology: Similarity in characteristics resulting from shared ancestry.
      • Owen's interpretation of homology: Similarity in structures despite differences in function, focusing on ideal forms.
      • Darwin's interpretation of homology: Similarity of characters due to traits inherited from a common ancestor, emphasizing evolutionary relationships.
      • Understanding homology is crucial for modern research, particularly in fields like comparative genomics and developmental biology.

Natural Selection

• Mentioned as a key mechanism driving descent with modification.

Evolutionary Tree-Thinking (Phylogenetics)

• Historical Context:
  • First conceptualized by Charles Darwin in his notebook in 1837.
  • Later visualized by Ernst Haeckel in 1891.
• Importance:
  • Helps estimate the origin and timing of evolutionary events, such as the SIV-HIV jump to humans.
  • Defines "cousin" relationships based on the number of generations since a last common ancestor.
• Key Definitions:
  • Phylogeny: The evolutionary history (represented as a tree) of a group of organisms.
  • Lineage: A sequence of ancestor to descendant populations through time.
    • Evolution involves the separation (diversification) of lineages.
    • Each branch on a phylogeny represents a lineage.
    • Lineages can be living (extant) or extinct.
• Uses of Phylogenies:
  • Biological Classification: Organizing life forms into hierarchical groups (Order, Family, Genus, Species).
    • Example: Panthera pardus (leopard) in the Felidae family, within the Carnivora order.
  • Understanding Historical Relationships:
    • Resolving relationships using genetic data (e.g., mitochondrial DNA, nuclear DNA, DNA/DNA hybridization).
    • Example: Tracing the evolution of domestic dogs from wolves.
    • Constructing the "Tree of Life" for all organisms on Earth.
    • Studying the historical relationships between languages.
  • Forensics: Determining the origin and transmission of pathogens.
    • Case Study: Using phylogenetic analysis of HIV sequences to investigate whether a Florida dentist infected his patients.
  • Biogeography & Adaptation: Investigating correlations between speciation events and geological or ecological changes.
  • Gene Duplication and Gene Families: Understanding the evolutionary history of genes within a genome.
  • Tracing Origins of Human Disease: Identifying the source and evolutionary pathway of pathogens.
    • Example: Phylogeny of SARS-CoV-2 receptor binding domains indicates a possible bat origin (2020 study by Lau et al.).

How to Read and Infer Phylogenies

• Basic Structure: Phylogenetic trees visually represent descendants diverging from common ancestors.
• Representation: Trees can be drawn in various formats (e.g., rectangular, diagonal, circular), but the underlying relationships (topology) can be equivalent.
  • Tree Equivalency: Different tree drawings can represent the same evolutionary history.
• Nature of Phylogenies: Phylogenies are hypotheses about evolutionary relationships, based on available evidence.
  • They are visual representations of descent with modification from a common ancestor.
• Inferring Phylogenies (Ideal Case):
  • Characters: Traits used to compare organisms.
  • Derived Character: A trait that is present in one or more descendant species but was NOT present in their common ancestor.
    • Shared Derived Characters: Traits shared by a group of descendants from a common ancestor who developed the trait.
    • Unique Derived Characters: A derived trait found only in a single terminal taxon (or a very small group not forming a larger clade).
  • Nested Sets of Shared Derived Characters: Evolutionary relationships are often revealed by characters that are shared at different levels of a hierarchy.
  • Clades: Groups of taxa that include an ancestor and all of its descendants.
    • Identified by shared derived traits.
    • Example: In a hypothetical tree, a "BLUE clade" might be species with orange wing-tips, indicating their common ancestry for that trait.
  • Synapomorphy: Another name for a shared derived character; it is a derived character shared by two or more taxa and inherited from their most recent common ancestor. It is key to defining clades.