Phylogenetic Networks of SNPs with Constrained Recombination D. Gusfield, S. Eddhu, C. Langley.
Phylogenetic Networks - DIMACS
Transcript of Phylogenetic Networks - DIMACS
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PhylogeneticPhylogenetic NetworksNetworks
Daniel H. HusonDaniel H. Huson
wwwwww--ab.informatik.uniab.informatik.uni--tuebingen.detuebingen.de
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PhylogeneticPhylogenetic NetworksNetworksAs a data representation As a data representation techniquetechnique
Splits graphs and othersSplits graphs and others
As a more complex As a more complex model of evolutionmodel of evolution
Reticulation graphs: Reticulation graphs: such as hybridization such as hybridization graphs or ancestor graphs or ancestor recombination graphsrecombination graphs
xx11 xx33 xx44 xx99 xx1010xx22
xx55
xx88xx66
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PhylogeneticPhylogenetic NetworksNetworks
Rooted splits graphRooted splits graph UnrootedUnrootedreticulation graphreticulation graph
Either type of graph can be Either type of graph can be unrootedunrooted or rootedor rooted
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What is a Splits Graph?What is a Splits Graph?
The The split encodingsplit encoding ΣΣ(T) of a tree T:(T) of a tree T:
GG11
GG88
GG77
GG66
GG55
GG44
GG33GG22
GG11,G,G33,G,G44,G,G66,G,G77 vsvs GG22,G,G55,G,G88
eeGG88
GG55GG22
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What is a Splits Graph?What is a Splits Graph?
CutCut--set of parallel edges defines split {set of parallel edges defines split {A,BA,B} } vsvs restrest
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GlossaryGlossarySplits system Splits system ΣΣ: a set of splits : a set of splits ((bipartitioningsbipartitionings) of a given ) of a given taxontaxon set Xset XSplits graph GSplits graph G: graph representing : graph representing ΣΣ(includes trees, not necessarily planar!)(includes trees, not necessarily planar!)SplitsTreeSplitsTree: a program providing various : a program providing various algorithms for computing splits graphsalgorithms for computing splits graphsSplit decompositionSplit decomposition: an algorithm for : an algorithm for computing splits from distancescomputing splits from distances(other: (other: NeighborNeighbor--Net, consensus networks, Net, consensus networks, or Zor Z--super networks)super networks)
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Example: Consensus NetworksExample: Consensus NetworksSix input trees:Six input trees:
ΣΣ((1/6):1/6): ΣΣ((0):0):ΣΣ((1/2):1/2):
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SplitsTree4 SplitsTree4
Provides many Provides many algorithms for algorithms for
phylogeneticphylogenetic analysis analysis using trees and using trees and
networksnetworks
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The The SplitsTreeSplitsTree ProgramProgram
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The The SplitsTreeSplitsTree ProgramProgram
TaxaTaxaUnalignedUnalignedCharactersCharactersDistancesDistancesQuartetsQuartetsTreesTreesSplitsSplits
Main WindowMain Window
Method WindowMethod Window
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Example: ZExample: Z--Super NetworkSuper NetworkFive trees fungal trees from Five trees fungal trees from (Pryor 2000) and (Pryor 2003)(Pryor 2000) and (Pryor 2003)Trees:Trees:
ITS (two trees)ITS (two trees)SSU (two trees)SSU (two trees)GpdGpd (one tree)(one tree)
Numbers of Numbers of taxataxa differ: “partial trees”differ: “partial trees”Trees from Trees from TreeBaseTreeBase
Unfortunately, no edge lengthsUnfortunately, no edge lengths
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Individual Gene TreesIndividual Gene Trees
ITS00ITS00
46 46 taxataxa
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Individual Gene TreesIndividual Gene Trees
ITS03ITS03
40 40 taxataxa
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Individual Gene TreesIndividual Gene Trees
SSU00SSU00
29 29 taxataxa
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Individual Gene TreesIndividual Gene Trees
SSU03SSU03
40 40 taxataxa
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Individual Gene TreesIndividual Gene Trees
Gpd03Gpd03
40 40 taxataxa
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Gene Trees as Super NetworkGene Trees as Super Network
ZZ--closure: a fast superclosure: a fast super--network method (WABI 2004)network method (WABI 2004)
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Gene Trees as Super NetworkGene Trees as Super Network
ITS00+ITS00+ITS03ITS03
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Gene Trees as Super NetworkGene Trees as Super Network
ITS03+ITS03+SSU00SSU00
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Gene Trees as Super NetworkGene Trees as Super Network
ITS00+ITS00+ITS00+ITS00+SSU03SSU03
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Gene Trees as Super NetworkGene Trees as Super Network
ITS00+ITS00+ITS03+ITS03+SSU03+SSU03+Gpd03Gpd03
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Gene Trees as Super NetworkGene Trees as Super Network
ITS00+ITS00+ITS03+ITS03+SSU00+SSU00+SSU03+SSU03+Gpd03Gpd03
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ZZ--Super NetworkSuper Network
AA22
BB22
Idea: Idea: ExtendExtend partial splits.partial splits.
ZZ--rule:rule:
Repeatedly apply to completion. Repeatedly apply to completion. Return all full splits.Return all full splits.
AA11
BB11
AA22
BB22
AA11
BB11∪ ∪ BB22
AA11 ∪ ∪ AA22
BB22
∩∩
,,
AA11
BB11
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Reticulation NetworksReticulation Networks
aabb11 cc bb33
bb22
hh
PP QQ
Ancestral genomeAncestral genomegg11
Build gene treesBuild gene trees
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Reticulation NetworksReticulation Networks
PP
gg11PP--treetree
hhbb1 aa cc bb331
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Reticulation NetworksReticulation Networks
PP
gg22
hhaabb11 cc bb33
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Reticulation NetworksReticulation Networks
PP
gg22QQ--treetree
hhaabb11 cc bb33
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From Gene Trees to Reticulation GraphsFrom Gene Trees to Reticulation Graphs
gene tree1gene tree1 gene tree2gene tree2 combinedcombinedsplits
reticulationreticulationgraphsplits graph
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Multiple Independent ReticulationsMultiple Independent Reticulations
Two hybridizations Two hybridizations ⇒⇒four different gene trees
reconstructedreconstructedreticulationsall splitsall splits reticulations
four different gene trees
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NonNon--Independent Reticulation EventsIndependent Reticulation Events
base treebase tree
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Splits GraphSplits Graph
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Reticulation GraphReticulation Graph
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Reticulation GraphReticulation Graph
Ambiguous,Ambiguous,unless root in unless root in
{t{t55,t,t66} or {b} or {b11,…,b,…,b44}}
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Application to Real Data: ButtercupsApplication to Real Data: Buttercups
ITS (nuclear genome)ITS (nuclear genome) JSA (chloroplast genome)JSA (chloroplast genome)
jointly with Pete Lockhartjointly with Pete Lockhart
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Application to Real Data: ButtercupsApplication to Real Data: Buttercups
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Application to Real Data: ButtercupsApplication to Real Data: Buttercups
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Algorithm to Detect Reticulation Algorithm to Detect Reticulation •• Input: set of splits Input: set of splits ΣΣ•• Process each component of the Process each component of the
incompatibility graph IG(incompatibility graph IG(ΣΣ) separately) separately•• Generate all possible “linear” Generate all possible “linear”
reticulation scenariosreticulation scenarios•• Check necessary conditions on splitsCheck necessary conditions on splits•• Check sufficient conditions on splitsCheck sufficient conditions on splits•• Modify splits graph to display Modify splits graph to display
detected reticulationsdetected reticulations
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Splits Graphs and ReticulationsSplits Graphs and Reticulations
XXAA
BB11 BB22 BB33 BB44
XXCC
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Recognizing an Isolated ReticulationRecognizing an Isolated Reticulation
XX
BB11 BB22 BB33 BB44
uu1 uu3uu2 uu41 32 4
AA CC
AABB11 BB22 BB33 BB44
XX
dd2dd1 dd3 dd421 3 4
CC
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Recognizing an Isolated ReticulationRecognizing an Isolated Reticulation
The associated splits graph…The associated splits graph…
BB11 BB22 BB33 BB44
XX
uu11 uu22 uu33 uu44dd11 dd22 dd33 dd44
uu11
dd33 uu22
uu33
uu44
dd44
dd22
dd11
AA CC
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Splits Graph to Reticulation GraphSplits Graph to Reticulation Graph
The associated splits graph…
BB22 BB33
AA CC
BB44BB11
The associated splits graph…
Delete all Delete all internal edgesinternal edges
XX
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Splits Graph to Reticulation GraphSplits Graph to Reticulation Graph
& the reticulation graph
AA
XX
Delete all Delete all internal edgesinternal edges
CC
BB44BB33BB11 BB22
The associated splits graph…The associated splits graph… & the reticulation graph
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Reconstruction From Mosaic SequencesReconstruction From Mosaic Sequences
Mosaic sequences evolvingMosaic sequences evolvingalong two different treesalong two different trees
Splits graph containingSplits graph containingthe splits of both treesthe splits of both trees
NeighborNeighbor--netnet
As sequences grow longerAs sequences grow longer
AA
BB
CCDD
EEff
eeAA
BB
CC
DDEE
AABB
CC DDEE
ee
ff
NeighborNeighbor--net consistentnet consistenton circular distanceson circular distancesGalled trees always circularGalled trees always circularBryant, Huson, Bryant, Huson, KloepperKloepper and and NieseltNieselt, WABI 2003, WABI 2003
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SummarySummarySplits graphs and reticulation networks Splits graphs and reticulation networks are different, but related types of are different, but related types of phylogeneticphylogenetic networksnetworksBased on this, algorithms for detecting Based on this, algorithms for detecting and visualizing “linear” reticulation and visualizing “linear” reticulation scenarios can be developedscenarios can be developedImplementations exist and will be made Implementations exist and will be made available in available in SplitsTreeSplitsTree
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AcknowledgementsAcknowledgementsTobias Tobias KloepperKloepper and Mike Steel and Mike Steel (hybridization detection algorithms)(hybridization detection algorithms)Pete Lockhart (application to plants)Pete Lockhart (application to plants)Dave Bryant (SplitsTree4)Dave Bryant (SplitsTree4)
Software: wwwSoftware: www--ab.informatik.uniab.informatik.uni--tuebingen.detuebingen.de