Comprehensive Study Notes on Phylogeny and the Tree of Life

Cellular Organisms Without Cell Nuclei

  • Cellular organisms without cell nuclei include Prokaryotes:
    • Bacteria ("stick"; single cell; no nucleus)
    • Archaea ("old"; single cell; no nucleus)

Major Groups of Organisms

  • Chromalveolates
  • Rhizaria
  • Green Plants
    • Bryophytes
    • Embryophytes
  • Vascular Plants
    • Xylem and Seeds
    • Spermatophytes (Enclosed Seeds)
      • Angiosperms ("receptacle-seed")
      • Eudicots
      • Dicots
      • Monocots

Tree of Life

  • Opisthokonta
  • Cnidaria (radial symmetry)
  • Animalia (Metazoa: "beyond animals")
    • Arachnids (8 legs)
  • Various plant types:
    • Brown algae, kelp (Phaeophyceae)
    • Diatoms ("cut in two"; algae: plankton)
    • Radiolarians ("small sunbeam"; protozoa)
    • Foraminiferans ("hole bearers"; plankton)
    • Green algae (Chlorophyta)
    • Mosses (Bryophyta)
    • Liverworts (Marchantiophyta)
    • Ferns (Filicophyta)
    • Cycads (Cycadophyta) [seeds]
    • Conifers (Coniferae) [cones]
    • Other flowering plants (laurels, magnolias, etc.)

Major Animal Groups

  • Metazoans ("beyond animals")
    • Eumetazoa ("good animals")
    • Bilateral symmetry (e.g., Arthropods)
      • Protostomes: First opening in cell cluster becomes mouth
      • Deuterostomes: Second opening in cell cluster becomes mouth

Classification of Organisms

Phylogeny

  • Phylogeny refers to the evolutionary history of a species or a group of related species.
  • Legless lizards and snakes share common ancestry with legged lizards but evolved independently.
  • Systematics is the discipline that classifies organisms based on their evolutionary relationships.

Binomial Nomenclature

  • Developed by Carolus Linnaeus in the 18th century:
    • Species are given two-part names called binomials.
    • The first part is the genus (capitalized).
    • The second part is the specific epithet (italicized).
    • Together, they name the species.

Hierarchical Classification

  • Organisms are grouped into increasingly inclusive categories:
    • Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.
  • A taxon is a taxonomic unit at any level of hierarchy.
  • Broader taxa across lineages are not directly comparable in genetic diversity.

Phylogenetic Trees

  • Phylogenetic trees illustrate evolutionary relationships:
    • Each branch point signifies the divergence of two species.
    • The trees can rotate around branch points without altering relationships.
    • Sister taxa share an immediate common ancestor.

Types of Taxa

  • A rooted tree shows a branch representing the last common ancestor of all taxa.
  • A basal taxon diverges early in a group's history, found near the common ancestor.
  • Polytomy describes a branch from which multiple groups emerge.

Limitations of Phylogenetic Trees

  • Trees depict descent patterns, not phenotypic similarity.
  • They do not indicate the timing of species evolution or the extent of change.
  • Do not assume a taxon evolved directly from the adjacent taxon in the tree.

Morphological and Molecular Data

  • Morphological and molecular homologies:
    • Homologies are phenotypic and genetic similarities due to shared ancestry.
    • When determining phylogeny, it is crucial to distinguish between homology and analogy.

Convergent Evolution

  • Convergent evolution leads to analogous structures across different evolutionary lineages, due to similar environmental pressures.

Analyzing Molecular Homologies

  • Systematists analyze DNA and morphology to classify organisms.
  • Homology can be distinguished by fossil evidence, complexity, and shared characters.

Cladistics

  • Cladistics organizes species by common descent.
  • Valid clades are monophyletic, containing an ancestor and all its descendants.
  • Paraphyletic groups miss some descendants; polyphyletic groups include species without their common ancestor.

Shared Ancestral and Derived Characters

  • Shared ancestral characters predate taxon divergence; derived characters are unique to a clade.

Phylogenetic Tree Construction and Characteristics

  • Outgroups help differentiate ancestral from derived characteristics.
  • Trees may indicate genetic change or evolutionary time based on branch lengths.

Molecular Clocks in Evolution

  • Uses constant rates of gene evolution to estimate the timeline for evolutionary changes.
  • Regularities can be disrupted by natural selection.

Applying Molecular Clocks

  • Molecular clocks show divergence times, as seen with HIV's evolution.

Evolutionary Classification

  • Early classifications varied from two kingdom systems to the current three-domain system: Bacteria, Archaea, Eukarya.
  • The role of horizontal gene transfer complicates classification and evolutionary relationships.
  • Gene transfers between organisms can blur lineages, suggesting early life forms are interconnected.