Phylogeny & the Tree of Life

• phylogeny


  the evolutionary history of a species or group of related species
• To understand the phylogeny of a species, biologists use systematics
• systematics


  a scientific discipline focused on classifying organisms & determining their evolutionary relationships
• binomial


  the two-part Latinized name of a species consisting of the genus & specific epithet; introduced in the 18th century by Carolus Linnaeus
• genus


  a taxonomic category above the species level, designated by the first word of a species' two-part scientific name
• The second part of a binomial is called the specific epithet and is unique for each species within a genus
• Hierarchical Classification

  A) Kingdom

  B) Domain

  C) Phylum

  D) Class

  E) Order

  F) Family

  G) Genus

  H) Species

  
• taxon


  a named taxonomic unit at any given level of classification
• phylogenetic tree


  a branching diagram that represents a hypothesis about the evolutionary history of a group of organisms
• Parts of a Phylogenetic Tree

  A) sister taxa

  B) polytomy

  C) basal taxon

  D) branch point

  E) root

  
• branch points


  the representation on a phylogenetic tree of the divergence of two or more taxa from a common ancestor
• sister taxa


  groups of organisms that share an immediate common ancestor
• root


  a branch point within the tree (typically farthest to the left) that represents the last common ancestor
• polytomy


  a branch point from which more than two descendant groups emerge
• homology


  similarity due to shared ancestry
• analogy


  similarities due to convergent evolution
• Analogous structures that arose independently are also called homoplasies
• molecular systematics


  a scientific discipline that uses nucleic acids or other molecules in different species to infer evolutionary relationships
• Comparing nucleic acids in distantly related species is challenging because they typically have different bases at many sites and can have different lengths. This is due to insertions and deletions accumulating over long periods of time.
• cladistics


  an approach to systematics in which organisms are placed into groups called clades based primarily on common descent
• clade


  a group of species that includes an ancestral species & all of its descendants
• monophyletic


  pertaining to a group of taxa that consists of a common ancestor & all of its descendants (equivalent to a clade)
• paraphyletic


  pertaining to a group of taxa that consists of a common ancestor & some, but not all of its descendants
• polyphyletic


  pertaining to a group of taxa derived from two or more different ancestors
• Label the Types of Groups

  A) monophyletic

  B) paraphyletic

  C) polyphyletic

  
• shared ancestral character


  a character, shared by members of a particular clade, that originated in an ancestor that is not a member of that clade
• shared derived character


  an evolutionary novelty that's unique to a particular clade
• In order to determine the clade where a character first appeared, we must select an outgroup
• outgroup


  a species or group of species from an evolutionary lineage that's known to have diverged before the lineage that contains the group of species being studied
• We can determine which characters were derived at various branch points by comparing members of the ingroup to each other and the outgroup
• ingroup


  a species or group of species whose evolutionary relationships we seek to determine
• maximum parsimony


  a principle that states that when considering multiple explanations, one should first investigate the simplest explanation that's consistent w/ the facts (aka Occam's razor)
• The most parsimonious tree requires the fewest evolutionary events
• maximum likelihood


  a principle that states that when considering multiple phylogenetic hypotheses, one should take into account the hypothesis that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time
• phylogenetic bracketing


  an approach in which features shared by two groups of organisms are predicted to be present in their common ancestor & all of its descendants
• Gene duplications can increase the number of genes in a genome, allowing for more evolutionary change
• orthologous genes


  homologous genes that are found in different species because of speciation
• paralogous genes


  homologous genes that are found in the same genome as a result of gene duplication
• molecular clock


  a method for estimating the time required for a given amount of evolutionary change, based on the observation that some regions of genomes appear to evolve at constant rates
• We can calibrate the molecular clock of a gene by graphing the number of genetic differences against the dates of branch points