Lecture 7

• Individuals


  Reproduce, giving rise to successive generations within a population
• Populations


  Consist of interbreeding individuals that persist over many generations, creating a genetic continuity
• Species


  Can comprise multiple populations, which might be interconnected through gene flow (i.e., migration and mating)
• Populations of an ancestral species

  Can diverge, leading to the formation of new species, some of which may go extinct
• Phylogenies


  Trace the evolutionary history and relationships of species, showing how multiple species are connected through common ancestry
• Phylogenetic trees


  • Are hypotheses depicting the evolutionary relationships among taxa (e.g., species)
  • Time progresses from the root to the tips
  • Lineages that share more recent common ancestors are considered more closely related
  • Terminal nodes represent taxa currently under study
  • Internal nodes represent hypothesized common ancestors, each of which splits into two (or more) descendant lineages
  • The root represents the hypothesized common ancestor of all taxa in the tree

  
• Ways to draw a phylogenetic tree

  • Horizontally or vertically
  • Curved lines or straight
  • Radial (i.e., circular) trees
  • Polytomy – internal node with >2 descendant branches, usually indicating uncertainty in branching order
• A phylogeny is like a child's mobile
• Left and right have no inherent meaning in a phylogeny, or top and bottom if the tree is drawn horizontally
• All that matters is the branching pattern, which denotes the relationships
• The tree preserves its meaning, even if it is rotated around one of its internal nodes
• Equivalent phylogenies


  • Three coloured trees showing the same relationships
  • Two vertebrate phylogenies showing the same relationships

  
• Conventional placement of humans at the bottom (or right) of a phylogeny might be incorrectly interpreted as suggesting humans are more advanced or are an endpoint of evolution
• Homology


  Inheritance of a trait from a common ancestor
• Homoplasy


  Independent evolution of a trait

  
• Types of homoplasy


  • Convergent evolution – independent evolution of a trait, typically caused by adapting to similar habitats/niches
  • Reversal – trait reverts to an ancestral form
• Homoplasy causes similarities between distantly related species, which complicates phylogenetic tree-building
• The best characters for building a phylogenetic tree are hard-to-evolve characters that are unlikely to have evolved twice or to have been lost

  
• Clade


  A monophyletic group - a set of taxa comprising an ancestor and all its descendants
• Synapomorphies


  Shared, derived characters that identify clades - evolutionary novelties shared by two or more (but not all) species currently under consideration

  
• "Enlarged brain" is not a synapomorphy as it is not shared (i.e., it is unique to humans)
• "Skull, brain, spine" is not a synapomorphy as they are not derived (i.e., the common ancestor of all taxa under consideration had them)</b>
• Monophyletic


  Group (clade) comprises a common ancestor and all its descendant taxa
• Polyphyletic


  Group comprises various taxa but not their common ancestor; therefore, the group has multiple origins
• Paraphyletic


  Group comprises various taxa and their common ancestor, but not all the common ancestor's descendant taxa
• In modern Biology, taxonomic groupings must be monophyletic
• Many traditionally defined taxa, such as fish and reptiles, are no longer considered valid because they are not monophyletic
• To be made monophyletic, they must be redefined (e.g., so that Reptilia includes birds)
• Ways of inferring a phylogenetic tree

  • Neighbor-joining – algorithm for producing a short tree by iteratively grouping most similar taxa
  • Maximum parsimony – search for the tree that requires the fewest changes
  • Maximum likelihood – search for the tree that best explains the data (based on a model of evolution)
  • Bayesian – search for the tree that is most likely to be true (based on the data and some prior information)
• Statistical support for the branching pattern

  • Bootstrap support (NJ, MP, ML)
  • Clade credibility (Bayesian)
• Maximum parsimony


  • Considers the tree requiring the fewest changes to be the "best" tree
  • Tries to maximize similarities due to homology and minimize similarities due to homoplasy
  • Philosophy related to Ockham's razor
• Tree 1 is the most-parsimonious tree because it requires the fewest changes and has no homoplasy
• Trees 2 & 3 have convergent evolution of TàA at Site 3 in Species 3 & 4
• Outgroup


  Used to root the phylogenetic tree and determine the direction of evolution

  
• LUCA – last universal common ancestor
• B – endosymbiotic event where an ancestral eukaryotic cell engulfed a bacterium, leading to the evolution of mitochondria
• C – endosymbiotic event where an ancestral eukaryotic cell (already containing mitochondria) engulfed a bacterium, leading to the evolution of chloroplasts
• Reticulated evolution


  Phylogenies that are not strictly dichotomous, and may include reticulation (i.e., joining of separate lineages)

  
• Causes of reticulation


  • Horizontal gene transfer – movement of genetic material between organisms by non-vertical (i.e., parent–offspring) transmission
  • Hybrid speciation – formation of a new species from interbreeding of two distinct species
• The early "tree of life" is probably more like a tangled bush due to endosymbiosis, etc.