Phylogenetics

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

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: 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

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

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

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