evolution exam 4

• There may still be some character conflict, even after applying these methods
• Determining synapomorphies


  1. Collect data set

  2. Go to parsimony if there is character conflict

  3. Continue to collect data and refine analysis of already collected traits

  4. Once the phylogeny is constructed, reassign conflicting characters to symplesiomorphic or analogous status

  
• Rooting a tree


  1. Outgroup comparison

  2. Embryological criterion (Only useful for multicellular organisms)

  3. Paleontological criterion (Mostly for organisms with hard body parts)
• Any tree can be rooted except the complete tree of life, unless you are very clever about gene duplication
• Where the root goes is very important as it can significantly change what we think about how a set of species evolved
• Molecular method


  • Collect character states (nucleotides and amino acids)
  • Each nucleotide/amino acid in a sequence is a character
  • Each is considered independent of the others, with some exceptions
• We have to go straight to parsimony when using the molecular method as there is no means of determining homologies and analogies
• Determining homologies


  1. Homologous characters show the same fundamental structure

  2. Homologies have the same fundamental relationships to surrounding characters

  3. Same embryonic development in different species

  
• Using parsimony to construct an unrooted tree

  1. First need to align sequences for analysis

  2. Look for positional homology

  3. Leave out areas of uncertainty

  4. Follow the rules of parsimony

  5. Write out all possible phylogenies and choose the one with the least number of steps
• Positional homology is demonstrated by preserving the alignment of characters across sequences
• Sequence Alignment


  1. Positional homology preserved

  2. Positional homology not preserved

  
• Correct alignment


  • Positional homology preserved
• Incorrect alignment


  • Positional homology not preserved
• Substitution


  Replacement of one nucleotide with another
• Insertion


  Addition of a nucleotide
• Deletion


  Removal of a nucleotide
• Use Parsimony to Construct an Unrooted Tree
• Root the tree
• Only outgroup (OG) comparison is available for ordering character states
• Only rarely have molecular fossils
• No embryological development of NT and AA
• Figure out the most parsimonious branch for adding the outgroup
• Just add OG to every branch and see which adds the fewest number of steps
• Can lead to problems if multiple roots are equally compatible
• The number of combinations is enormous even with a relatively small number of taxa
• Can only search exhaustively through trees for about 30 spp
• When there are too many trees to search, we employ heuristics to search the "tree space" for the optimal solution
• Example of human mitochondrial tree: 189 human mitochondria sequenced, produced 135 unique mitochondrial types, after one run it suggested an African origin of humans, other runs showed other origins
• Need almost as many synapomorphies as taxa to be resolved, preferably more
• Case of mt again: 119 synapomorphies for 135 tips
• Can have several results compatible with the evidence because not enough characters to distinguish them
• Need to pick a molecule that evolves at an appropriate rate

  
  

  Too slow: not enough information to resolve the phylogeny

  Too fast: too many analogous changes to make sense of the relationship

  Parsimony assumption violated
• Accounting for phylogeny, the evolution of a trait like the vertebrate eye may have only occurred once, with that adaptation then inherited by descent in many species
• About 1500 species of cacti, but only one origin of spines for the group - 1500 spiny species from one event
• Analogies (independently evolved similar traits) provide better evidence for adaptation when considering phylogenetic relationships
• Discrete character traits


  Character traits that have qualitatively discrete states
• Continuous (quantitative) character traits


  Characters that have continuous distributions
• Discrete character trait analysis

  1. Generate phylogeny using other characters

  2. Map putative adaptive trait and suspected selective agent onto phylogeny

  3. Infer where and how often trait evolved using parsimony or maximum likelihood

  4. Infer where and how often selective agent changed

  5. More independent origins of trait with selective agent = stronger evidence for adaptation
• Repeated evolution of a trait with the selective agent does not prove adaptation - there may be genetic or environmental correlations
• Undocumented extinct species can influence estimates of number and timing of character changes, more likely to miss adaptations than identify false ones