BME 130 – Genomes Lecture 3 Sequencing technology I The bad old days.
BME 130 – Genomes Lecture 26 Molecular phylogenies I.
-
date post
20-Dec-2015 -
Category
Documents
-
view
217 -
download
2
Transcript of BME 130 – Genomes Lecture 26 Molecular phylogenies I.
BME 130 – Genomes
Lecture 26
Molecular phylogenies I
Cacao genome sequenced
http://www.cacaogenomedb.org/
A phylogeny
How can we construct a phylogeny?
Convergent evolution (homoplasy)
apomorphicplesiomorphicplesiomorphic
Molecular phylogenies with sequence data
Benefits?
Number of trees# taxa # unrooted
trees# rooted trees
3 1 3
4 3 15
5 15 105
6 105 945
7 945 10395
8 10395 135135
9 135135 2027025
10 2027025 34459425
Outgroup can root a tree
Anc: ACGTCGAGTTATTA
A: ATGTCGGGTTATTA
B: ACGTCGAGTCATTC
C: ACGCTGAGTCATTA
Patterson and Reich (2006) Nature
441(7097):1103
Sequence alignment is necessary for phylogenetic analysis
Distance methods for phylogenetic reconstruction:UPGMA: pick two closest nodes, collapse, continueNeighbor-joining (NJ): pick two nodes that minimize total branch length, collapse, continue
Bootstrapping to measure robustness of phylogenetic tree
Phylogenetic methods that search tree-space
Maximum parsimony: correct tree is the one requiring the fewest changes
Maximum-likelihood: p(D|tree, M)
The molecular clock