evolutionary analysis. tree mathematical structure model evolutionary history
TRANSCRIPT
Evolutionary Analysis
Tree
Mathematical structure
Model evolutionary history
Taxon 1
Taxon 2
Taxon 3
Taxon 4
Taxon 5
Taxon 6
Taxon 1
Taxon 2
Taxon 3
Taxon 4
Taxon 5
Taxon 6
Sister taxa
Outgroup
Root
Branch
Node
Tip
Polytomy (more than one branch emerging from one node)
(a) The astragalus is a synapomorphy that identifiesartiodactyls as a monophyletic group.
Camel
Peccary
Pig
Hippo
Whale
Deer
Cow
Astragalus(ankle bone)
ARTIODACTYLS
Gain of pulley-shaped astragalus
(b) If whales are related to hippos, then two changesoccurred in the astragalus.
Camel
Peccary
Pig
Hippo
Whale
Deer
Cow
ARTIODACTYLS
Gain of pulley-shaped astragalus
Loss of pulley-shaped astragalus
(a) The astragalus is a synapomorphy that identifiesartiodactyls as a monophyletic group.
(b) If whales are related to hippos, then two changesoccurred in the astragalus.
Camel
Peccary
Pig
Hippo
Whale
Deer
Cow
Camel
Peccary
Pig
Hippo
Whale
Deer
Cow
(c) Data on the presence and absence of SINE genes support the close relationship between whales and hippos.
Cow
Locus
DeerWhaleHippoPigPeccaryCamel
Astragalus(ankle bone)
1 gene present0 gene absent? still undetermined
Whales and hippos share fourunique SINE genes (4, 5, 6, and 7)
ARTIODACTYLS
ARTIODACTYLS
Gain of pulley-shaped astragalus
Loss of pulley-shaped astragalus
Gain of pulley-shaped astragalus
Phylogenetic Tree
shows ancestor-descendent relationships among populations or species
clarifies evolutionary relationships
Root
Ancestor of all sequences on tree
Taxon 1
Taxon 2
Taxon 3
Taxon 4
Taxon 5
Taxon 6
Sister taxa
Outgroup
Root
Branch
Node
Tip
Polytomy (more than one branch emerging from one node)
Taxon 1
Taxon 2
Taxon 3
Taxon 4
Taxon 5
Taxon 6
Taxon 1
Taxon 3
Taxon 2
Taxon 4
Taxon 5
Taxon 6
(a) (b) (c)1
2
3
4
5
6
1
6
5
4
3
2
2
4
5
6
3
1
(a) (b) (c)1
2
3
4
5
6
1
6
5
4
3
2
2
4
5
6
3
1
= =
Types of Trees
Rooted
Unrooted
Rooted Trees
Node identified as root, from which all other nodes descend
Have direction corresponding to evolutionary time
Taxon 1
Taxon 2
Taxon 3
Taxon 4
Taxon 5
Taxon 6
Sister taxa
Outgroup
Root
Branch
Node
Tip
Polytomy (more than one branch emerging from one node)
Unrooted Trees
Lacks root
Does not specify evolutionary relationships
Nothing about ancestors and descendents
Unrooted Trees
Lacks root
Does not specify evolutionary relationships
Nothing about ancestors and descendents
Many tree-building programs generate unrooted trees!
Types of Trees
Cladogram
Phylogram
Cladogram
Cladogram
Relative recency of common ancestry
Cladogram
Cladogram
Relative recency of common ancestry
Does not show amount of evolutionary change
Phylogram
Phylogram
Also contains branch lengths
Numbers associated with branches
Amount of evolutionary change
Phylogram
Cladogram
Phylogram
Constructing a Tree
Construct multiple sequence alignment
Build Tree
Evaluate Tree
So how do I build a tree?
So how do I build a tree?
http://www.phylogeny.fr/
http://expasy.org/tools/
http://evolution.genetics.washington.edu/phylip/software.html#methods
Tree building programs
Tree drawing programs
FASTA alignment
Newick Format
(((((((Prochlorococcus_marinus:0.499642,Synechococcus_BL107:0.212828)0.961000:0.131562,Cyanobium_PCC7001:0.279338)0.984000:0.159534,Thiomicrospira_crunogena:0.805902)0.230000:0.067881,Allochromatium_vinosum:0.522452)0.974000:0.136543,(Bradyrhizobium_BTAi1:1.004711,Nitrobacter_hamburgensis:0.728510)0.596000:0.070606)0.895000:0.088934,Halothiobacillus_neapolitanus:0.624513)0.987000:0.172336,Acidimicrobium_ferrooxidans:0.338388,Acidithiobacillus_ferrooxidans:0.255268);
Tree drawing programs
File formats to save your tree
Evaluating Trees
Do your results make sense?
Evaluating Trees
Do your results make sense?
resample your data
Bootstrap treebranch support values
Evaluating Trees
Do your results make sense?
resample your data
ground-truth your data
www.ncbi.nlm.nih.gov
Organism Trees vs Gene Trees
Don’t always match!
Homologs
Orthologs
separated by speciation
Paralogs
produced by gene duplication
Xenologs
result of horizontal gene transfer
Tree-building resources
http://www.phylogeny.fr/
http://expasy.org/tools/
http://evolution.genetics.washington.edu/phylip/software.html#methods