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Splits and Phylogenetic Networks SplitsSplits andand PhylogeneticPhylogenetic NetworksNetworks DanielDaniel H.H. HusonHuson Paris, June 21, 2005 1 ContentsContents 1.1. PhylogeneticPhylogenetic treestrees 2.2. SplitsSplits networksnetworks 3.3. ConsensusConsensus networksnetworks 4.4. HybridizationHybridization andand reticulatereticulate networksnetworks 5.5. RecombinationRecombination networksnetworks 2 PhylogeneticPhylogenetic NetworksNetworks Bandelt (1991): Network displaying evolutionary relationships Other types of Splits Phylogenetic Reticulate phylogenetic networks trees networks networks Median Consensus Hybridization Recombination Augmented networks (super) networks networks trees networks Special case: “Galled trees” Any graph Ancestor Split decomposition, representing Split decomposition, recombination evolutionary Neighbor-net graphs data 3 PhylogeneticPhylogenetic NetworksNetworks 22 11 Other types of Splits Phylogenetic Reticulate phylogenetic networks trees networks networks 33 44 55 Median Consensus Hybridization Recombination Augmented networks (super) networks networks trees networks from sequences Special case: “Galled trees” from trees Any graph Ancestor Split decomposition, representing Split decomposition, recombination evolutionary Neighbor-net graphs data from distances 4 PhylogeneticPhylogenetic NetworksNetworksDan Gusfield: “Phylogenetic network” 22 11 “Generalized Other types of Splits Phylogenetic Reticulate phylogeneticphylogenetic networks trees networks network”networks 33 44 \ 55 Median Consensus Hybridization Recombination“More generalizedAugmented networks (super) networks networks trees networks Phylogenetic network” from sequences Special case: “Galled trees” from trees Any graph Ancestor Split decomposition, representing Split decomposition, recombination evolutionary Neighbor-net graphs data from distances 5 PartPart II 1.1. PhylogeneticPhylogenetic treestrees 2.2. SplitsSplits networksnetworks 3.3. ConsensusConsensus networksnetworks 4.4. HybridizationHybridization andand reticulatereticulate networksnetworks 5.5. RecombinationRecombination networksnetworks 6 PhylogeneticPhylogenetic TreesTrees Ernst Haeckel, Tree of Life 1866 7 PhylogeneticPhylogenetic TreesTrees LetLet XX == {x{x1,...,x,...,xn}} denotedenote aa setset ofof taxa.taxa. AA phylogeneticphylogenetic treetree TT (or(or XX--treetree)) isis givengiven byby labelinglabeling thethe leavesleaves ofof aa treetree byby thethe setset X:X: Cow Fin Whale Blue Whale Habor Seal Rat Mouse Chimp Human Gorilla Taxa + tree ⇒ phylogenetic tree 8 UnrootedUnrooted vsvs RootedRooted TreesTrees Unrooted tree Rooted tree, rooted using Chicken as outgroup mathematically and algorithmically biologically relevant, defines easier to deal with clades of related taxa 9 AA SimpleSimple ModelModel ofof EvolutionEvolution TAA G C CG T ACT C CG A T AC GC C time time AC C C A G C T Evolutionary tree AC G C C T •Mutations along branches •Speciation events at nodes A C Sequence of common ancestor 12 TreeTree ReconstructionReconstruction ProblemProblem TAA G C CG T AC T C CG A T AC GC C Tree? Evolutionary tree 13 TreeTree ofof LifeLife BasedBased onon 16S16S rRNArRNA (Doolittle, 2000) 14 PartPart IIII 1.1. PhylogeneticPhylogenetic treestrees 2.2. SplitsSplits networksnetworks 3.3. ConsensusConsensus networksnetworks 4.4. HybridizationHybridization andand reticulatereticulate networksnetworks 5.5. RecombinationRecombination networksnetworks 15 SplitsSplits NetworksNetworks RepresentsRepresents incompatibleincompatible signalssignals inin data,data, from:from: SequencesSequences,, e.g.:e.g.: Median network (Bandelt et al 1994) Spectral analysis (Hendy and Penny 1993) DistancesDistances,, e.g.:e.g.: E.g. Split decomposition (Bandelt and Dress 1992) Neighbor-Net (Bryant and Moulton 2002) TreesTrees,, e.g.:e.g.: Consensus network (Holland and Moulton 2003) Super network (H., Dezulian, Kloepper and Steel 2004) Bootstrap network (H., implemented in SplitsTree4) 16 SequencesSequences toto SplitsSplits NetworkNetwork If characters have only 2 states and not too conflicting: interpret columns as splits and draw full splits network 17 DistancesDistances toto SplitsSplits NetworkNetwork Split decomposition or Neighbor-Net produces network from distances 18 TreesTrees toto SplitsSplits NetworkNetwork A collection of trees can be represented by a consensus network or super network 19 BootstrapBootstrap NetworkNetwork Draw all splits that have positive bootstrap score 20 SplitSplit DecompositionDecomposition && BootstrapBootstrap NetworkNetwork CompareCompare thethe resultresult ofof SplitSplit DecompositionDecomposition withwith anan NJNJ treetree andand bootstrapbootstrap network:network: A.cerana A.mellifer A.cerana A.mellifer A.cerana A.mellifer A.dorsata A.dorsata A.dorsata A.andrenof A.andrenof A.florea A.andrenof A.koschev A.florea A.koschev A.florea A.koschev Bio-NJ tree Bootstrap network Splits network obtained via the Split Decomposition Bill Martin: Splits networks show which signals tree reconstruction methods are fighting over… 21 RootedRooted SplitsSplits NetworksNetworks Splits network can be “rooted” e.g. using an outgroup (Gambette and H, manuscript) 22 BetterBetter layoutlayout ofof splitssplits networksnetworks Philippe Gambette, currently visiting Tuebingen from ENS Cachan 23 PartPart IIIIII 1.1. PhylogeneticPhylogenetic treestrees 2.2. SplitsSplits networksnetworks 3.3. ConsensusConsensus networksnetworks 4.4. HybridizationHybridization andand reticulatereticulate networksnetworks 5.5. RecombinationRecombination networksnetworks 24 GeneGene TreesTrees CanCan DifferDiffer AlsoAlso allowallow genegene duplicationduplication andand lossloss:: x1 x2 x3 A’ A” B’ x x x A’ A’’ B’ x1 x2 x3 ≠ A B Gene duplication Gene Tree Species Tree G 25 GeneGene TreesTrees vsvs SpeciesSpecies TreesTrees Differing gene trees give rise to “mosaic sequences” Gene A Gene B Gene C Gene D 26 ConsensusConsensus ofof DifferentDifferent GeneGene TreesTrees ForFor aa givengiven setset ofof species,species, differentdifferent genesgenes leadlead toto differentdifferent treestrees HowHow toto formform aa consensusconsensus ofof thethe trees?trees? ConsensusConsensus treestrees ConsensusConsensus networksnetworks ConsensusConsensus supersuper networksnetworks 27 TheThe SplitsSplits ofof aa TreeTree EveryEvery edgeedge ofof aa treetree definesdefines aa splitsplit ofof thethe taxontaxon setset X:X: x6 x4 x1 x 8 e x5 x3 x7 x2 xx ,x,x ,x,x ,x,x ,x,x vsvs xx ,x,x ,x,x 1 3 4 6 7 2 5 8 28 TheThe SplitSplit EncodingEncoding ofof aa TreeTree dd aa Tree T: cc bb ee Split encoding Σ(T): 5 trivial splits: 2 non-trivial splits: 29 CompatibilityCompatibility TwoTwo splitssplits AA1|B|B1 andand AA2|B|B2 ofof XX areare compatiblecompatible,, ifif ∅∈∅∈{A{A1∩∩AA2,,AA1∩∩BB2,B,B1∩∩AA2,B,B1∩∩ AA2}} Two compatible splits: A1 B1 x x4 A2 B2 x3 x8 x7 8 x2 x9 x5 x 1 x 6 X 30 CompatibilityCompatibility TwoTwo splitssplits AA1|B|B1 andand AA2|B|B2 ofof XX areare compatiblecompatible,, ifif ∅∈∅∈{A{A1∩∩AA2,A,A1∩∩BB2,B,B1∩∩AA2,B,B1∩∩ AA2}} Two incompatible splits: x x4 A1 B1 x5 A2 x6 B2 x2 x3 X x1 X 1 x7 31 ConsensusConsensus ofof TreesTrees Six gene trees: Σ(1/2): majority consensus: Σ(1/6): Σ(0): splits contained in more splits contained in splits contained than 50% of trees more than one tree in at least one tree 34 ExampleExample ofof AA SuperSuper NetworkNetwork (Plants)(Plants) Partial trees for five plant genes Super network 35 Joint work with Kim McBreen and Pete Lockhart ZZ--ClosureClosure MethodMethod Idea:Idea: ExtendExtend partialpartial splits.splits. ∩ A A ∪ A ZZ--rule:rule: A1 A2 1 1 2 , B1 B2 B1∪ B2 B2 B RepeatedlyRepeatedly applyapply 1toto completion.completion. A2 ReturnReturn allall fullfull splits.splits. A1 B2 [Huson, Dezulian, Kloepper and Steel, 2004] 36 ExampleExample FiveFive fungalfungal treestrees fromfrom [[Pryor,Pryor, 2000]2000] andand [Pryor,[Pryor, 2003]2003] Trees:Trees: ITSITS (two(two trees)trees) SSUSSU (two(two trees)trees) GpdGpd (one(one tree)tree) NumbersNumbers ofof taxataxa differ:differ: “partial“partial trees”trees” 37 ExampleExample 4beta25: User manual now available from www.splitstree.org! 38 IndividualIndividual GeneGene TreesTrees ITS00 46 taxa 39 IndividualIndividual GeneGene TreesTrees ITS03 40 taxa 40 IndividualIndividual GeneGene TreesTrees SSU00 29 taxa 41 IndividualIndividual GeneGene TreesTrees SSU03 40 taxa 42 IndividualIndividual GeneGene TreesTrees Gpd03 40 taxa 43 GeneGene TreesTrees asas SuperSuper NetworkNetwork Z-closure: a fast super-network method 44 GeneGene TreesTrees asas SuperSuper NetworkNetwork ITS00+ ITS03 45 GeneGene TreesTrees asas SuperSuper NetworkNetwork ITS03+ SSU00 46 GeneGene TreesTrees asas SuperSuper NetworkNetwork ITS00+ ITS00+ SSU03 47 GeneGene TreesTrees asas SuperSuper NetworkNetwork ITS00+ ITS03+ SSU03+ Gpd03 48 GeneGene TreesTrees asas SuperSuper NetworkNetwork ITS00+ ITS03+ SSU00+ SSU03+ Gpd03 49 PartPart IVIV 1.1. PhylogeneticPhylogenetic treestrees 2.2. SplitsSplits networksnetworks 3.3. ConsensusConsensus networksnetworks 4.4. HybridizationHybridization andand reticulatereticulate networksnetworks 5.5. RecombinationRecombination networksnetworks 50 HybridizationHybridization OccursOccurs whenwhen twotwo organismsorganisms fromfrom differentdifferent speciesspecies interbreedinterbreed andand combinecombine theirtheir genomesgenomes Copyright © 2003 University of Illinois Copyright © 2003 University of Illinois Copyright © 2003 University of Illinois Water hemp Hybrid Pigs weed 51 SpeciationSpeciation byby HybridizationHybridization
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