Application of Phylogenetic Networks in Evolutionary Studies

Daniel H. Huson and David Bryant

Presented by Peggy Wang

The plan

Terminology Split networks:

What are they? How can they be interpreted? Phylogenetic inference

SplitsTree4

A tree of terms..

Terminology

phylogenetic networkany network in which taxa are represented by nodes and their evolutionary relationships are represented by edges

Types of networks phylogenetic tree

Leaf labeled tree that represents the evolutionary history of a set of taxa, possibly with branch(edge) lengths, either unrooted or rooted.

reticulate networkPhylogenetic tree + additional edges. Nodes with more than two parents represent reticulate events such as hybridization, recombination and hgt

split networkRepresents incompatible and ambiguous signals in a data set. Parallel edges represents splits computed from data. Incompatible splits may result in nodes that do not represent ancestral species.

Wait… whats a split again? split

A partition of the taxa into two nonempty subsets, such as the partition obtained when we remove a branch from a phylogenetic tree.

split network (formally)For a given taxon set X and set of splits S, we define a split network N to be a connected graph in which some of the nodes are labeled by taxa and all edges are labeled by splits.

Removing all edges associated with a given split s in S divides N into two connected components, one part containing all taxa on one side of S and the other part containing all taxa on the other side.

The edges along any shortest path in N are all associated with different splits.

A split network contains exactly the same information as a list of splits with a weight for each split.

Every split network represents a unique collection of splits.

A given collection of splits can have many different split network representations.

The interpretation of the network depends on how the splits were constructed and assigned weights…

Interpreting Split Networks: Representing multiple trees

We can use split networks to summarize a large collection of trees. Code each individual tree as a collection

of splits Define a summary set of splits Represent the set using a split network.

Consensus networks Constructed from all splits appearing in

at least some fixed proportion of input trees

Interpreting Split Networks:Representing multiple trees Confidence sets

Assign an interval for the weights of each split

A tree is contained within the split network N if

(1) Every split in the tree is a split in the network

(2) For every split in the tree, the corresponding branch length is contained within the corresponding interval

(3) For every split in the network not in the tree, the assigned interval contains zero.

.

N

Interpreting Split Networks:Representing multiple trees

Geometric interpretation:

Index splits from 1 to m.

Tree can be coded as a point in m-dimensional space: the ith coordinate is the length of the ith split, or 0 if that split is not present in the tree.

Interpreting Splits Networks:Networks and systematic error

Sampling error

Random error resulting from a small sample size (number of sites).Deal with these errors using nonparametric bootstrap, multiple samples from posterior distribution

Systematic error

Mistakes in the assumptions of a model or method which cause data to be misinterpreted. Likely to occur with large, multigene, heterogeneous data sets. How to deal with these errors?

Interpreting Splits Networks:Networks and systematic error

Phylogenetic inference(1) Construct a split network using the best

available model and method.(2) Determine if the network is significantly

different from a tree.(3) If the tree is significantly non-treelike, then

there is probably an error in the model. If possible, improve the model and try again.

(4) If the network is treelike, and there is no significant sampling error, the continue with a tree-based phylogenetic analysis.

Reticulate Networks

2 disagreeing trees

Split network represents all splits present in either of the two trees

Reticulate network

Explains the differences in the two trees using 3 reticulation events

SplitsTree4 Integrates a wide range of phylogenetic network and

phylogenetic tree methods, inference tools, data management utilities, and validation methods.

Included methods for inferring split networks: From character data. Median networks, parsimony

splits, spectral analysis From distance matrices. Split decomposition and

neighbor-net From sets of trees. Consensus networks and

supernetworks. Also constructs other types of phylogenetic networks,

eg recombination and hybridization networks User friendly?!

Example 1:Heterogeneous Evolution

Jukes-Cantor

p=0.75

q=0.05

0<r<0.4

Example 2:Animal Phylogeny

Coelomate hypothesis

Ecdysozoa hypothesis

More examples..Dusky dolphins 60 variables (sites of DNA)

35 haplotypes

Neighbor-joining tree with bootstrap values

Consensus network of 3 MP trees

Split decomposition network

95% confidence network Median network Neighbor-net network

Conclusion!

Split networks are useful for visualization.

However they are not useful for making conclusive phylogenetic analysis.

SplitsTree4 encompasses many tools, but are they really that useful?