Phylogenetics

Introduction to Phylogenetics

Phylogenetics: the study of the evolutionary history and relationships among groups of organisms

• Tree of Life Diagram Charles Darwin Origin of Species; phylogenetic tree

Pedigrees and Phylogenies:

• Pedigree: general term that refers to the historical relationship between individual organisms
• Phylogeny: describes evolutionary history of the relationships among groups of living things
• Phylogenetic Tree: diagrammatic representation of this evolutionary history in the form of a tree
  • Uses morphological, behavioral, biochemical, genetic factors to show evolutionary history
  • ONLY ONE TRUE PHYLOGENY, which is unknown

Systematics:

• Systematics: study and classification of living organisms
• Great Chain of Being (scala naturae): strict hierarchical structure of life, beginning with God and progressing to angels, animals, plants, minerals
  • God created this hierarchy
• After Darwin, scientists began to use data to infer the historical relationships
• Two methods:
  • Phenetics: study of relationships among organisms based on the degree of similarity among them, relies on convenient observable characteristics, does not necessarily reflect on genetic similarity or evolutionary relatedness
  • convergent evolution
  • Cladistics: approach to biological classification in which organisms are grouped together in monophyletic groups (clades) based on their most recent common ancestor
  • superior to phenetics

Illustrating the Concepts with Hypothetical Phylogeny

• Modification through mutation and genetic recombination gives rise to genetic diversity
• Character (trait): organisms material feature
  • ex: pattern, color, shape
• Character state (trait value): value of the character in the organism
  • ex: Individual 1 is solid gray circle
• Derived trait: one that is evolved from an earlier condition, called an ancestral trait
• When constructing phylogenetic trees, group taxa with homologous traits together
• Homologous trait/homology: any heritable trait shared by more than one species and inherited from a common ancestor
• Synapomorphies: shared, derived traits that provide evidence of common ancestry
• Homoplasies: traits that are shared not due to a common evolutionary history but rather because of convergent evolution or evolutionary reversal
  • Convergent evolution: occurs when similar traits evolve in different lineages due to similar evolutionary pressures
  • Evolutionary reversals: occurs when a character reverts from a derived state back to an ancestral state
• Outgroup: a species closely related to the ingroup, but not closely related enough to be inside the group of interest

The Parsimony Principle:

• Parsimony principle: states that the simplest explanation for observed data is the best explanation
  • Most parsimonious explanation = requires fewest untested assumptions

Applications of Phylogenetics

• Phylogenies are useful for answering evolutionary questions:
  • Estimating how long ago a trait evolved
  • Clarifying the sequence in which traits evolved
  • Examining relationships among organisms
  • Determining when and where traits have evolved independently
• Applications:
  • Medical forensics
  • HIV
  • Determining the evolution of a sexually selected trait
  • Swordfish

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