Newer methods for tree building

• Parsimony analysis• Maximum likelihood• Bayesian inference

• For all 3: Build an unrooted tree on one of these three criteria, ignore synapomorphy and symplesiomorphy, and pull root out on tree using outgroup

All computationally intense

Newer methods for tree buildingSearch Criteria

• Parsimony Analysis = build unrooted tree with the fewest character state changes

• Maximum likelihood = given rules about how DNA sequences change over time, a tree can be found that reflects the most likely sequence of events

• Bayesian inference = generates a posterior distribution for a parameter, composed of a phylogenetic tree and a model of evolution, based on the prior for that parameter and the likelihood of the data

Pretty hard to do by hand…

Rooted vs. unrooted trees

Basal node obvious vs. basal node unknownRooted trees are way more fun!

Just need to know which node is basal (oldest) Imagine pulling strings

A B C D

e f

g

A

B

C

D

e f

Rooted vs. unrooted trees

Basal node obvious, basal node unknown

Number of unrooted trees for 4 taxa = 3A

B

C

D

A

C

B

D

A

D

C

B

Number of unrooted trees for 4 taxa = 3Number of rooted trees for 4 taxa = 15

A

B

C

D

A

C

B

D

A

D

C

B

Practice rooting

UnrootedTree of HerpesViruses

Number of trees increases with number of taxa

• 4 taxa 3 unrooted trees• 8 taxa 10,395 unrooted trees• 10 taxa 2,027,025 unrooted trees• 22 taxa 3 x 1023 (almost a mole)• 50 taxa 3 x 1074 (More trees than the number of

atoms in the universe)• “Exhaustive searches” of tree topologies are nearly

impossible with modern data sets • Algorithms attempt to find best tree anyway

Barry Hall, Phylogenetic Trees Made Easy

Estimating confidence in trees:

• Character conflict is common in data. We want to know if it is overwhelming the signal in the data.

• We may not have collected enough data to estimate relationships confidently.

Estimating confidence in trees:

• Bootstrap support• If low, mentally collapse the node into a

polytomy

Breaking the Bifurcation Rule:Hard polytomies and Soft polytomies

Cichlids

Venereal syphilis

http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0002303

195050-100 millionpeople

Non-venereal Trepanomatoses

1950

Non-venereal Trepanomatoses

195050-100million

1970

Endemic Trepanomatoses

1990 = 2.5 million