Phylogenetics

• Systematics: study of diversity/evolutionary relationships
• Taxonomy (describing/naming/classifying)   * Nested hierarchy (domain -> species)    * Taxon (taxa pl.): general name for group @ any level    * Domain, kingdom, phylum, class, order, family, genus, species (King Phillip came over for great spaghetti)    * binomial nomenclature: two-name naming system where species = basic unit
• Linking taxonomy and phylogeny   * Linnaean classification/phylogeny can differ from each other   * Phylogeny (includes evolutionary history): groups with common ancestor and all descendants   * Phylogenetic species concept: smallest set of organisms that can be distinguished into phylogenetic tree (how much ancestry shared/how much evolution occurred) 
• Basics of phylogenetics (Intro)   * Phylogenetic tree: branching diagram; pattern of descent; hypothesis about evolutionary relationships    * Dichotomies: 2-way branch points   * Extant species: alive, tips of branches
• How to read a phylogeny    * Rooted tree: represents most recent common ancestor of all taxa on tree   * Basal taxon: diverges early/originates near common ancestor (Ex: ancestor more like leopard, fewest changes) -> note that ancestors don’t have all char. Of descendants   * Branch point: divergence of 2 species from common ancestor   * Sister taxa: 2 taxa share immediate common ancestor (most recently related)    * Polytomy: >2 groups emerge from 1 branch    * Monophyletic: includes ancestor/all descendants     * All members of group share common ancestor, trace evolutionary relationships   * Paraphyletic grouping (missing descendants, common ancestor included): common ancestry and some but not all descendants, not a natural evolutionary grouping    * Polyphyletic grouping (wrong descendants, common ancestor is missing): doesn’t include most recent common ancestor and misrepresents evolutionary relationships 
• Making phylogenetics: inferred from molecular/morphological traits   * Cladistics: groups organisms by common descent/ancestry    * Clade: group including ancestral species/all descendants 
• General methods    * Homology (homologous): derived from common ancestor   * Analogies (analogous characteristics): not good for phylogenies     * Convergent evolution (independently acquired) bc of similar evolutionary pressure; not from same ancestor    * Homologies are good characteristics to build tree; all characters in phylogeny must result from homology (bat/bird wings are homologous as forelimbs, analogous as functional wings) -> divergent    * Shared ancestral characters: char. Of group present in ancestors that remain present in descendants    * Shared derived characters: char. Unique to particular clade; originates in recent CA and present in all descendants    * Outgroup: taxa diverged before lineage being studied   * Ingroup: taxa being studied   * Recent development use programs/math to analyze relationships (primary structure of proteins--DNA, mRNA sequence/molecular similarities: same pattern to distinguish homology from analogy) 

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