Notes on Phylogeny and Evolution

Learning Objectives

  • Types of Evidence for Evolutionary Relationships
    • Evidence includes morphology, genes, and biochemical data.
  • Phylogenetic Trees and Cladograms
    • Tools for inferring evolutionary relationships.

Phylogeny

  • Definition:
    • The evolutionary history of a species or group of related species, often illustrated as a branching diagram (tree of life).
  • Systematics:
    • The scientific study of classifying organisms and determining their evolutionary relationships.
  • Phylogenetic studies aim to understand how species are related based on their shared ancestry.

Taxonomy and Naming

  • Taxonomy:
    • The scientific discipline for classifying and naming organisms.
  • Binomial Nomenclature:
    • A two-part naming system introduced by Carolus Linnaeus.
      • Genus: First part, capitalized.
      • Specific Epithet: Second part, unique to each species, italicized.
  • Hierarchical Classification:
    • Levels from broad to narrow: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.
    • Taxon: Any group at any level of the hierarchy.

Constructing Phylogenetic Trees

  • Phylogenetic Tree:
    • A diagram representing evolutionary relationships.
    • Branch Points: Indicate divergence between two species.
  • Sister Taxa:
    • Groups sharing an immediate common ancestor.
  • Rooted Trees:
    • Include a branch to represent the last common ancestor.
  • Basal Taxon:
    • The lineage that diverged earliest in the history of a group.

Patterns of Descent

  • Phylogenetic Trees:
    • Show patterns of descent, not phenotypic similarity.
    • They do not indicate timing of evolution or magnitude of change.

Homologies and Analogies

  • Homology:
    • Similarity due to shared ancestry.
  • Analogy:
    • Similarity due to convergent evolution where unrelated species adapt similarly.
  • Examples:
    • Bat and bird wings are homologous as forelimbs but analogous as functional wings.

Evaluating Molecular Homologies

  • Molecular Analysis:
    • Systematists analyze DNA sequences to determine evolutionary relationships, utilizing computer programs for accuracy.

Cladistics

  • Cladistics:
    • Method grouping organisms by common descent.
  • Clade:
    • A group that includes an ancestral species and all of its descendants.
  • Monophyletic, Paraphyletic, Polyphyletic Groups:
    • Monophyletic: Includes all descendants of a common ancestor.
    • Paraphyletic: Excludes some descendants.
    • Polyphyletic: Includes species with different ancestors.

Shared Characters

  • Shared Ancestral Characters:
    • Traits that originated in an ancestor of the taxon.
  • Shared Derived Characters:
    • Traits that evolved in a more recent ancestor and are unique to particular clades.

Inferring Phylogenies**

  • Outgroup Comparison:
    • Use an outgroup to differentiate between shared ancestral and derived characters.

Molecular Clocks**

  • Use constant rates of evolution to estimate the timing of evolutionary changes.
  • Molecular changes are calibrated against known fossil records.

Horizontal Gene Transfer**

  • The movement of genes between organisms in different domains, complicating our understanding of evolutionary relationships.
  • Prominent in prokaryotes and eukaryotes due to various mechanisms of gene exchange.