Terminology of phylogenetic treesTypes of phylogenetic treesTypes of DataCharacter EvolutionApproaches to Phylogeny Reconstruction

Phylogenetic tree (dendrogram)

Nodes: branching pointsBranches: linesTopology: branching pattern

Sister Taxa: two taxa that are more closely relatedto eachother than either is to a third taxon.

A + B

C + D

Branches can be rotated at a node, without changing therelationships among the OTU’s.

Levels of Resolution on a Phylogenetic Tree

Hard polytomy: simultaneous divergence.Soft polytomy: lack of resolution.

Rooted: unique path from root.Unrooted: degree of kinship, no evolutionary path.

Number of possible phylogenetic trees

3 OTU’s: 1 unrooted tree3 rooted trees

4 OTU’s: 3 unrooted trees15 rooted trees.

TYPES OF TREES

Newick (shorthand) format

- text based representation of relationships.

Qualitative vs. quantitative data

Quantitative: continuous data (i.e.height or length)

Qualitative: discrete (2 or more values)Binary: 2 values

Mulitstate: more than 2 values

Most molecular data are qualitativeBinary: presence or absence of band, or gap in sequence

Multistate: nucleotide data (A, T, G, C)

Nucleotide character data

Characters: position in the nucleotide sequence.(i.e. position 352)

Character states: nucleotide at the positionin the nucleotide sequence.(G, A, T, or C)

Unordered: change from one character toanother occurs in one step.(i.e. nucleotide changes)

Ordered: number of steps from one stateto another equals the absolute value ofthe difference between their state number.

1 2 3 4 5 requires 4 steps5 4 3 2 1 requires 4 steps

(reversible vs. unreversible)

Assumptions About Character Evolution

Phylogenetic reconstruction methods take into assumption:

(1) # of discrete steps required for one character state to change into another

(2) probability with which such change occurs.

Step matrix

- number ofsteps requiredbetween characterstates.

Approaches to Phylogeny Reconstruction

Cladistics (parsimony): recency of common ancestryMaximum Likelihood: model of sequence evolutionPhenetics (UPGMA, neighbor joining): overall similarity

Parsimony: General scientific criterion for choosing amongcompeting hypotheses that states that we should acceptthe hypothesis that explains the data most simply andefficiently.

Maximum parsimony method of phylogeny reconstruction:The optimum reconstruction of ancestral character states isthe one which requires the fewest mutations in the phylogenetictree to account for contemporary character states.

PARSIMONY APPROACH

First step in maximum parsimony analysis:Identify all of the informative sites.

Invariant: all OTU’s possess the same characterstate at the site.

Any invariant site is uninformative.

Two types of variable sites:

Informative: favors a subset of trees over other possible trees.Uninformative: a character that contains no groupinginformation relevant to a cladistic problem (i.e. autapomorphies).

Uninformative: each tree 3 steps

Parsimony Analysis 2nd step: Calculate the minimum numberof substitutions at each informative site

Informative: favors tree 1 over other 2 trees.

1 step 2 steps 2 steps

Final step in parsimony analysis: Sum the number of changes over all informative sites for each possible tree and choose the tree associated with the smallest number of changes.

Site 3

Site 4

Site 5

Site 9

3 steps 3 steps 4 steps

Parsimony Search Methods:

Exhaustive search method: searches all possible fully resolved topologies and guarantees that all of the minimum length cladograms will be found.(not a practical option, time consuming)

Branch and bound methods: begins with a cladogram. The lengthof starting cladogram is retained as an upper bound for useduring subsequent cladogram construction. As soon as a lengthof part of the tree exceeds the upperbound, the cladogram isabandoned. If equal length, cladogram is saved as an optimaltopology. If length is less, it is substituted for the original as the optimal upperbound. (good option for fewer than 20 taxa, time consuming)

Heuristic methods: approximate or “hill climbing technique”Begin with a cladogram, add taxa and swap branches until a shorter length cladogram is found. Procedure can be replicated many times to increase chance of finding minimum length cladogram.

Different types of parsimony analyses:

Unweighted parsimony: all character state changes aregiven equal weight in the step matrix.

Weighted parsimony: different weights assigned todifferent character state changes.

Transversion parsimony: transitions are completelyignored in the analysis, only transversions are considered.

Maximum Likelihood Method:

The likelihood (L) of a phylogenetic tree is theprobability of observing the data (nucleotide sequences)under a given tree and a specified model ofcharacter state changes.

The aim is to find the tree (among all possible trees)with the highest L value.

Models of character state changes (sequence evolution):

Jukes and Cantor 1 parameter model: all changes equal probabilityKimura 2 parameter model: transitions more frequent than

transversionsOther more complicated models…...

1. Calculate likelihoodfor each site on a specific tree.

2. Sum up the L values for all sites onthe tree.

3. Compare the Lvalue for all possibletrees.

4. Choose tree withhighest L value.

Distance Methods: evolutionary distances (number of substitutions)are computed for all pairs of taxa.

UPGMA: unweighted pairgroup method with arithmetic means- assumes equal rate of substitutions- sequential clustering algorithms- pairs of taxa are clustered in order of decreasing similarity

Neighbor Joining: finding shortest (minimum evolution) tree by finding neighbors that minimize the total length of the tree. Shortest pairs arechosen to be neighbors and then joined in distance matrix as one OTU.

Consensus Methods:

Consensus trees are derived from a set of trees andsummarize the phylogenetic information of severaltrees in a single tree.

Most commonly used consensus trees:

Strict consensus: all conflicting branching patterns arecollapsed.

50% majority rule consensus: branching patterns thatoccur with a frequency of 50% or more are retained,all others are collapsed.

ABCDE

FG

A

BC

DE

FG

A

BCD

E

FG

ABCDE

FG

ABCDE

FG

CONSENSUS METHODS

Bootstrap method of assessing tree reliability:

Inferred tree is constructed from data set. Characters are resampled from the data set with replacement. Resampling is replicated several (100-1000) times.

Bootstrap trees are constructed from the resampled data sets.

Bootstrap tree is compared to original inferred tree.

% of bootstrap trees supporting a node are determined foreach node in the tree.

Homoplasy: non-homologous similarity- resemblance not due to common ancestry- evolved independently- considered “noise”

Known bacterial phylogeny:ancestors at each node known.

Hillis & Huelsenbeck 1992tested the ability of different methods, of finding the “true” phylogeny.

Maximum parsimony andmaximum likelihood performedwell, UPGMA & neighborjoining did not.

Strengths and Weaknesses:

UPGMA & neighbor-joining: fast but not as accurate asother methods.

Maximum parsimony: time consuming, but more accurate.can combine morphological characters with DNA charactersin a single analysis.

Maximum likelihood: very time consuming, includinginformation from morphology is a new technique (but it iscontroversial), can invoke a specific model of sequence evolution.

Reference: Molecular Systematics 2nd Ed., Hillis et. al (1996), Sinauer Associates. ISBN:0-87893-282-8