Why use phylogenetic networks?
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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
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- to identify phylogenetic
relationships that are uncertain
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-to ask whether data are suitable for tree building
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another example: do Noppadon’s inversion distances give tree-like distances?
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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
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-to study complex processes (where sequence evolution at an individual
locus has not been tree like)
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- to study complex processes (where phylogenetic information from
different gene loci is incongruent)
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- to study complex processes (where phylogenetic information from
different gene loci is incongruent)
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R.nivicola
- to reconstruct reticulate
evolutionary models
origins of diploid and polyploid
hybrids
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Overview of phylogenetic network methods
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Median, split decomposition, NeighborNet
ACGACCTACGACTGCATCAGCATCGCATCAGCTACGCTCGCTCACGACCTACGACTGCATCAGCATCGCATCAGCTACGCTCGCTCAGACTATCGGATTAAAAGCATCAGCATCGACATCAGCATCAGCAGACTATCGGATTAAAAGCATCAGCATCGACATCAGCATCAGCGGCGCCATCGATCGCAATCAAGGGGGGGCCCTACCGCATTCAGGGCGCCATCGATCGCAATCAAGGGGGGGCCCTACCGCATTCAGCATCACGCTCGCCCAATCGCATCACGCATCGCATCGCATCGCACATCACGCTCGCCCAATCGCATCACGCATCGCATCGCATCGCATCGCATCGACTCGCATTCGCATCGACTCGCAT
ACGACCTACGACTGCATCAGCATCGCATCAGCTACGCTCGCTCACGACCTACGACTGCATCAGCATCGCATCAGCTACGCTCGCTCAGACTATCGGATTAAAAGCATCAGCATCGACATCAGCATCAGCAGACTATCGGATTAAAAGCATCAGCATCGACATCAGCATCAGCGGCGCCATCGATCGCAATCAAGGGGGGGCCCTACCGCATTCAGGGCGCCATCGATCGCAATCAAGGGGGGGCCCTACCGCATTCAGCATCACGCTCGCCCAATCGCATCACGCATCGCATCGCATCGCACATCACGCTCGCCCAATCGCATCACGCATCGCATCGCATCGCATCGCATCGACTCGCATTCGCATCGACTCGCAT
ACGACCTACGACTGCATCAGCATCGCATCAGCTACGCTCGCTCACGACCTACGACTGCATCAGCATCGCATCAGCTACGCTCGCTCAGACTATCGGATTAAAAGCATCAGCATCGACATCAGCATCAGCAGACTATCGGATTAAAAGCATCAGCATCGACATCAGCATCAGCGGCGCCATCGATCGCAATCAAGGGGGGGCCCTACCGCATTCAGGGCGCCATCGATCGCAATCAAGGGGGGGCCCTACCGCATTCAGCATCACGCTCGCCCAATCGCATCACGCATCGCATCGCATCGCACATCACGCTCGCCCAATCGCATCACGCATCGCATCGCATCGCATCGCATCGACTCGCATTCGCATCGACTCGCAT
Aligned sequencesAligned sequences
DistanceDistancematrixmatrix
Median network Median network splits graphsplits graph
Split decomposition & Split decomposition & NeighborNet network NeighborNet network splits graphsplits graph
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Consensus Networks and Super-Consensus Networks and Super-NetworksNetworks
Tree 1Tree 1 Tree 2Tree 2 Tree 3Tree 3
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site patterns, splits, splits graph
site patterns observed splits splits graph
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NJ
SD, NNET, MEDIAN network
calculated splits
8 site patterns
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extra site pattern
added
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nodes in splits graphs
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Different splits graphs – same splits
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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
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Splits graphs and reticulate evolutionary models
splits graphs explicit model of reticulate evolution
A H B CA H B C
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Building a reticulate evolutionary model
Z-closure Supernetwork
Hybridisation network
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Daniel Huson and David Bryant
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Split decomposition
• Identify weakly compatible splits for all possible combinations of quartets
• Define split lengths for all splits in split system
• Build splits graph
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An example of using distances to calculate the length of internal splits
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distance matrix calculated from sequences
• A• B 3 • C 6 5• D 5 6 9
AB|CD
AC|BD
AD|BC
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An example of using distances to calculate
the length of external splits
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example• A• B 3 • C 6 5• D 5 6 9
A|CD
A|BD
A|BC
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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
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All splits that have a circular ordering can be displayed in a
plane
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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
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Consensus networks
• Extends idea of median networks to splits calculated from trees
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106 random trees with 8 taxa
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Combining gene trees for 106 loci
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Supernetworks
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More detail about building a splits graph…..
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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
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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
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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!
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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
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Adding a Non-Circular Split
Want 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
•Duplicate intersectionDuplicate intersection
•Insert new split edgesInsert new split edges
xx11
xx77
xx44
xx22
xx66
xx55
xx33
xx11
xx77
xx44
xx22
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Adding a Non-Circular Split
Want 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
•Duplicate intersectionDuplicate intersection
•Insert new split edgesInsert new split edges
•Done!Done!
xx11
xx77
xx44
xx22
xx66
xx55
xx33
xx11
xx77
xx44
xx22
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