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