Evo bio CH 4

• how do we infer phylogeny? phylogenetic trees -

  • Uses statistical inference
  • Characters are statistical data: Morphology, Genetics, Behaviors 
• when comparing characters for phylogeny we must compare homologous traits 


  analogous structures: structures of different species with similar function

  homologous structures: structures developed from common ancestor

  
• Phylogenetic methods

  • Parsimony – trees that minimize number of evolutionary changes
  • Distance methods – counting number of commonalities
  • Maximum likelihood – statistical models to find how traits change
  • Baysian inference- statistical models of change, with interpretations of what is the best fit
• which tree is the most parsimonious?

  Both are the same in parsimony. Each has 3 steps

  
• Does mapping a single character difference for one species help?

  no

  
• What if we have more than one species with a shared difference?

  
equally parsimonious but one change (3) is more likely

  
• what if...

  • Two different trees have the same number of steps = equally parsimonious
  • Consensus tree – tree to represent multiple best phylogenies
  • Polytomy – relationship showing uncertainty

  
• Parsimony: The simplest explanation that fits the evidence is the most likely explanation.

  • Advantage = conceptual simplicity
  • Disadvantage = simplest is usually, but not always correct

  
• long - branch attraction

  • Evolution can occur at different rates
  • Rapidly evolving branches can infer too close a relationship
  • These long branches can pull together in inferring phylogeny

  
• distance methods

  • Uses measure of character differences between species
  • Goal is to find a tree where distance among branches equals distance measured between species
  • Proper alignment of data is critical
  • Method originally applied to phenetic data (species similarity data)
• what is the human most related to ?

  the mouse

  
• Measuring Distances:

  Straight-forward with genetic data

  • Align sequences
  • Count differences


  Morphological data

  • Measurements
  • Tally of different states
  • Only method for fossils
• Sequence Alignment

  Sometimes an easy process unless… mutations (Insertions, Deletions)

  
• Rooting a tree

  • Basal node (root) represents a common ancestor
  • Parsimony and distance methods find relationships but do not directly determine the root
  • Most common tool is to use an outgroup

  
• Ingroup – taxa of interest

  what is the common ancestor?

  
• outgroup

  • Closely related species
  • Is not part of ingroup
  • Presumed to share common ancestor with ingroup
  • below is azure winged magpie

  
• Derived vs. Ancestral characters

  • Using phylogeny we can infer evolutionary steps
  • Answer questions such as “what was the ancestral trait?”
  • Example: what was the ancestral beak color of our magpies

  
• how did it get a yellow beak?

  what is more likely, one change or three?

  black beak is plesiomorphic

  yellow beak is synapomorphic

  whole group is apomorphic

  
• Phylogeograpy – insight into radiation and movement of populations of a species.

  
• Problem: more species, more possible trees

  Question: at what point can’t you check trees one by one?

  ex: if there are 3 taxa there is 1 tree possible

  
• If we have a phylogeny, what does it tell us about the evolution of these species?

  The relationships and common ancestry among species.
• Can a phylogeny suggest natural selection occurrences?

  Yes.
• Are there associations between activities and habitats caused by natural selection?

  Yes.
• why would some plants have traits to make it burn better?

  Adaptation to fire, causes it to not completely kill the tree. Fire adapted traits and fire promoting traits