Lecture 5

Tree of Life

• Darwin's tree
• Origin of species - 1859 - variation and natural selection
• tree of life = universal tree
• gene tree explains phylogeny
  • det from gene dups, horiz gene transfer
• diversity in bact due to horiz gene transfer
  • transformation
  • transduction
• ernst haeckel's tree of life

Phylogenetic Tree

• tree topology
• gene tree doesn't reflect species tree
• mitochondria chloroplast are bacteria that entered eukaryotes
• ford dolittle tree of life
• tree huggers vs tree uprooters
  • tree of life is good, vs meaningless/horiz gene transfer
• operational taxonomic units
• node = common ancestor
• cladogram - depicts hypothesized evolutionary history
  • show branching order
  • branch length completely meaningless
• phylograms
  • both topology and branch length is informative
  • can say when event happened
• rooted vs unrooted trees
• rotated trees are identical
• 4 OTUs, 3 unrooted trees
  • look at outgroups to see what's closest to node, ancestor
• most difficult to root the trees
• genomes.urv.es/UPGMA/index.php

building trees

• Steps To Build A Phylogenetic Tree
• parsimony = defining topology of tree by trying to reduce the number steps required for phenotype.
• homoplasy = extra steps

test phylogenetic reliability

• bootstrap = statistic method to tell us how confident that two species belong to same group
• shuffling the columns
• [genomes.urv.es/UPGMA/index.php Website that makes dendrograms]
• Learn this - Cophenetic correllation wiki article
• Online bioinformatics tools from Pere's old lab