why use phylogenetic networks?

Why use phylogenetic networks?

• to visualize data when the evolutionary model is assumed to be bifurcating

• to visualize data when the evolutionary model may not be bifurcating

• to provide an analytical framework for studying processes that cause phylogenetic incongruence

• to build reticulate evolutionary models

- to identify phylogenetic

relationships that are uncertain

-to ask whether data are suitable for tree building

another example: do Noppadon’s inversion distances give tree-like distances?

NNET splits graph of angiosperm & gymnosperm sequences

Qui et al. 1999

[Mt: matR, atpI, Cp: atpB, rbcL, Nuc. 18sRNA]

-to help us understand why

some phylogenetic problems are hard

-to study complex processes (where sequence evolution at an individual

locus has not been tree like)

- to study complex processes (where phylogenetic information from

different gene loci is incongruent)

R.nivicola

- to reconstruct reticulate

evolutionary models

origins of diploid and polyploid

hybrids

Overview of phylogenetic network methods

Median, split decomposition, NeighborNet

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Aligned sequencesAligned sequences

DistanceDistancematrixmatrix

Median network Median network splits graphsplits graph

Split decomposition & Split decomposition & NeighborNet network NeighborNet network splits graphsplits graph

Consensus Networks and Super-Consensus Networks and Super-NetworksNetworks

Tree 1Tree 1 Tree 2Tree 2 Tree 3Tree 3

site patterns, splits, splits graph

site patterns observed splits splits graph

NJ

SD, NNET, MEDIAN network

calculated splits

8 site patterns

extra site pattern

added

nodes in splits graphs

Different splits graphs – same splits

summary

• Different reasons why you might want to build a phylogenetic network

• Some network methods identify more splits in the data than other methods

• there may be more than one splits graph representation for a set of splits

• Nodes in splits graph are not equivalent to the nodes in trees

Splits graphs and reticulate evolutionary models

splits graphs explicit model of reticulate evolution

A H B CA H B C

Building a reticulate evolutionary model

Z-closure Supernetwork

Hybridisation network

Daniel Huson and David Bryant

Split decomposition

• Identify weakly compatible splits for all possible combinations of quartets

• Define split lengths for all splits in split system

• Build splits graph

An example of using distances to calculate the length of internal splits

distance matrix calculated from sequences

• A• B 3 • C 6 5• D 5 6 9

AB|CD

AC|BD

AD|BC

An example of using distances to calculate

the length of external splits

example• A• B 3 • C 6 5• D 5 6 9

A|CD

A|BD

A|BC

NeighborNet (NNET)

• Use NeighborJoining like algorithms to determine the order in which sequences (nodes) can be joined to give a circular ordering.

• Once you have the circular ordering, use least squares to identify all splits with positive (non zero) lengths

• Build splits graph

All splits that have a circular ordering can be displayed in a

plane

Median networks

• Perform the median operation on all combinations of 3 sequences

• Identify all the splits between median and extant sequences – built a splits graph

Consensus networks

• Extends idea of median networks to splits calculated from trees

106 random trees with 8 taxa

Combining gene trees for 106 loci

Supernetworks

More detail about building a splits graph…..

Adding the Trivial Splits

• The set O of all trivial splits on X is represented by a star:

(Embedded graph: fixed circular ordering)

xx11

xx44

xx22xx33

xx55 xx77xx66

xx11

xx66

xx55

xx77

Adding a Circular Split

Want to add split Want to add split {{xx22,x,x33,x,x44} vs {} vs {xx11,x,x55,x,x66,x,x77}}

•Determine a path from Determine a path from xx22 to to xx44 along the fontier along the fontier of Gof G

•Separate componentsSeparate components

•Insert new split edgesInsert new split edgesxx44

xx33 xx22

xx44

xx33 xx22

xx11

xx66

xx55

xx77

Adding a Circular Split

xx66

xx55

xx33

xx11

xx77

xx44

xx22Want to add split Want to add split {{xx22,x,x33,x,x44} vs {} vs {xx11,x,x55,x,x66,x,x77}}

•Determine a path from Determine a path from xx22 to to xx44 along the frontier of along the frontier of GG

•Separate componentsSeparate components

•Insert new split edgesInsert new split edges

•Done!Done!

Adding a Non-Circular Split

xx66

xx55

xx33Want to add split Want to add split {{xx33,x,x55,x,x66} vs {} vs {xx11,x,x22,x,x66,x,x77}}

•Convex hull Convex hull {{xx33,x,x55,x,x66} }

•Convex hull {Convex hull {xx11,x,x22,x,x66,x,x77}}

•Determine intersectionDetermine intersection xx11

xx77

xx44

xx22

xx66

xx55

xx33

xx11

xx77

xx44

xx22

1111 1122

22 22

22

33

33

33

3344 44

44





•Determine intersectionDetermine intersection

•Duplicate intersectionDuplicate intersection


xx11

xx77

xx44

xx22

xx66

xx55

xx33

xx11

xx77

xx44

xx22





•Determine intersectionDetermine intersection

•Duplicate intersectionDuplicate intersection


•Done!Done!

xx11

xx77

xx44

xx22

xx66

xx55

xx33

xx11

xx77

xx44

xx22

why use phylogenetic networks?

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