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