Summarising Sets of Phylogenies Consensus Trees and Split/Consensus Networks Aidan Budd EMBL Heidelberg Friday July 2nd 2010 Basic Molecular Evolution.

Summarising Sets of Phylogenies Consensus Trees and Split/Consensus Networks Aidan Budd EMBL Heidelberg Friday July 2nd 2010 Basic Molecular Evolution Workshop: July 2010 BecA-ILRI Hub, Nairobi, Kenya Part 1 Thanks to... Sheila Mtakai Other course organisers and contributors EMBL and Toby Gibson (my supervisor) You for your participation! Consensus Trees and Split/Consensus Networks Any experience of using/building them? Can you describe any applications of them? A question for the participants... Example Applications: Comparing Trees Estimated with Different Methods Multilocus phylogeny of cichlid fishes (Pisces: Perciformes): evolutionary comparison of microsatellite and single-copy nuclear loci. Streelman, JT Zardoya, R Meyer, A Karl, SA Mol Biol Evol 1998 ;15(7): PMID: Do all East African cichlids share a unique common ancestor? Maximum Likelihood Maximum Parsimony Relatively 'easy' to ask this with just a few trees (2) each with few taxa (35) - more difficult with more trees and more taxa... Identifying agreement/similarity between tree topologies Example Applications: Comparing Trees Estimated from Different Loci Origin and biology of simian immunodeficiency virus in wild-living western gorillas. Takehisa JTakehisa J, Kraus MH, Ayouba A, Bailes E, Van Heuverswyn F, Decker JM, Li Y, Rudicell RS, Learn GH, Neel C, Ngole EM, Shaw GM, Peeters M, Sharp PM, Hahn BH.Ayouba A, Van He, Decker Rudicell RS, Leole EM, Stersarp PM, Hah J Virol Feb;83(4): PMID: F Figure 4: Copyright 2010 by the American Society for Microbiology. Copyri0 by the ciety fology. Is the simian immunodeficiency virus infecting Western lowland gorillas more closely related to viruses found in chimpanzees or in humans? Four trees estimated, one from each of four different HIV/SIV genes Gorilla Chimp Human Again, as in the previous slide - 'easy' to ask this with just a few trees (4) each with few taxa (25) - again, this is more difficult with more taxa and trees Identifying agreement/similarity between tree topologies Example Applications: Analysing Trees from Bootstrap/Bayesian Analyses Characterization of DrCol15a1b, a Novel Component of the Stem-Cell Niche in the Zebrafish Retina.Characterization of DrCol15a1b, a Novel Component of the Stem-Cell Niche in the Zebrafish Retina.Gonzalez-Nunez V, Nocco V, Budd A.Stem Cells Jun 14. PMID: Identifying clans with unambiguous phylogenetic signal in a set of sampled trees ML/npbs SuppFig3B SuppFig3C Example Applications: Analysing Trees from Bootstrap/Bayesian Analyses Bayesian Fig7 SuppFig3A Characterization of DrCol15a1b, a Novel Component of the Stem-Cell Niche in the Zebrafish Retina.Characterization of DrCol15a1b, a Novel Component of the Stem-Cell Niche in the Zebrafish Retina.Gonzalez-Nunez V, Nocco V, Budd A.Stem Cells Jun 14. PMID: Identifying clans with unambiguous phylogenetic signal in a set of sampled trees Example Applications: Analysing Trees from Bootstrap/Bayesian Analyses Homologous recombination as an evolutionary force in the avian influenza A virus.He CQ, Xie ZX, Han GZ, Dong JB, Wang D, Liu JB, Ma LY, Tang XF, Liu XP, Pang YS, Li GR.Mol Biol Evol Jan;26(1): PMID: Interpreting non-tree-like region of the split network as evidence for reticulate evolution (here recombination in viruses) Contribution of recombination and selection to molecular evolution of Citrus tristeza virus.Martn S, Sambade A, Rubio L, Vives MC, Moya P, Guerri J, Elena SF, Moreno P.J Gen Virol Jun;90(Pt 6): PMID: Martn SA, Rubio, Moya J, Elenno P.Jol ): Reticulate Networks The net of life: reconstructing the microbial phylogenetic network. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA. Genome Res Jul;15(7): PMID: Reconstructing the evolutionary history of polyploids from multilabeled trees. Huber KT, Oxelman B, Lott M, Moulton V. Mol Biol Evol Sep;23(9): PMID: Genetic exchange among natural isolates of bacteria: recombination within the phoA gene of Escherichia coli.DuBose RF, Dykhuizen DE, Hartl DL.Proc Natl Acad Sci U S A Sep;85(18): PMID: Describing evolutionary scenarios where some OTUs are believed to share multiple parental lineages HGT Hybridisation Recombination A B D Which of A B C and D is NOT equivalent to E? (i.e. has different topology) E f C Quiz - Identifying identical topologies A B D Which of A B C and D is NOT equivalent to E? (i.e. has different topology) E f C Quiz - Identifying identical topologies Splits Each branch of a tree describes a split of OTUs into two sets These sets correspond to the two clans associated with the branch e.g. black branch of the tree specifies the split ABCD | EFG can also be written ADCB | GFE etc. i.e. the taxon lists in the two halves of the split are unordered Splits Splits are either trivial example: F | ABCDEG associated with terminal branches provide no information about topology structure non-trivial example: ABCD | EFG associated with internal branches provide information about topology structure Exercise - Identify Splits For trees 1 and 2 below, write down the list of all non-trivial splits 1 2 Exercise - Identify Splits: ANSWERS 2 For trees 1 and 2 below, write down the list of all non-trivial splits 1 CB | EDAFEBC | DAF BDEC | AF HE | ABCDFGKMNPHEN | ABCDFGKMPDP | ABCEFGHKMNDPM | ABCEFGHKNDPMB | ACEFGHKNFK | ABCDEGHMNPFKG | ABCDEHMNPFKGC | ABDEHMNPFKGCA | BDEHMNP Splits Complete list of splits described by a tree allows reconstruction of that trees topology D F DF | ABCEGH A E BCDFGH | AE ABEGH | CDF C BH | ACDEFG BH G Helps to consider the sets of clans described by the splits Exercise - Reconstruct Topology from Set of Splits CB | ADEFGHKMNPEH | ABCDGHKMNPBCEH | ADFGKMNPFN | ABCDEGHKMPFNM | ABCDEGHKPFNMK | ABCDEGHPFNMKA | BCDEGHPGP | ABCDEFHKMNGPD | ABCEFHKMN 2 Draw the unique bifurcating unrooted tree topologies described by each of the two sets of splits, 1 and 2 EC | HNGAECH | GANGA | NHEC 1 Exercise - Reconstruct Topology from Set of Splits ANSWERS EC | HNGAECH | GANGA | NHEC CB | ADEFGHKMNPEH | ABCDGHKMNPBCEH | ADFGKMNPFN | ABCDEGHKMPFNM | ABCDEGHKPFNMK | ABCDEGHPFNMKA | BCDEGHPGP | ABCDEFHKMNGPD | ABCEFHKMN 2 1 Draw the unique bifurcating unrooted tree topologies described by each of the two sets of splits, 1 and 2 Ask your neighbour to check your answers, and discuss any disagreements you have between yourselves Exercise - Split Compatibility Sets (e.g. pairs) of splits are either: compatible a tree can be drawn that contains all splits in the set incompatible a tree cannot be drawn that contains all splits in the set Which of these sets of splits is incompatible? AB | CDEDE | ABC (i) BCDFGH | AEABEGH | CDF BG | ACDEFH (ii) AB | CDEAC | BDE (iii) i.e. for which set can you NOT build a tree which contains all the splits? Exercise - Split Compatibility: ANSWERS AB | CDEDE | ABC (i) BCDFGH | AEABEGH | CDF BG | ACDEFH (ii) AB | CDEAC | BDE (iii) Strict Consensus Trees iiiiiiivvviviiviii AB | CDEF******** 8 CD | ABEF** 2 EF | ABCD***** 5 ABC | DEF** 2 DE | ABCF* 1 CF | ABED** 2 ABD | ECF*** 3 ABF | CDE* 1 A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) AB C D F E Exercise - Strict Consensus Trees Draw the strict consensus tree for this set of 6 trees Begin by listing the set of splits found in the trees and counting their frequency Exercise - Strict Consensus Trees FG | ABCDE****** 6 BC | ADEFG****** 6 DE | ABCFG***** 5 ABC | DEFG***** 5 ADE | BCFG* 1 DFG | ABCE* 1 Trees Split Frequencies Draw the strict consensus tree for this set of 6 trees Begin by listing the set of splits found in the trees and counting their frequency Exercise - Strict Consensus Trees FG | ABCDE****** 6 BC | ADEFG****** 6 DE | ABCFG***** 5 ABC | DEFG***** 5 ADE | BCFG* 1 DFG | ABCE* 1 Trees Split Frequencies Draw the strict consensus tree for this set of 6 trees Begin by listing the set of splits found in the trees and counting their frequency 50%/Majority Rule Consensus Trees iiiiiiivvviviiviii AB | CDEF******** 8 CD | ABEF** 2 EF | ABCD***** 5 ABC | DEF** 2 DE | ABCF* 1 CF | ABED** 2 ABD | ECF*** 3 ABF | CDE* 1 A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) AB C D F E 5 8 50%/Majority Rule Consensus Trees iiiiiiivvviviiviii AB | CDEF******** 8 CD | ABEF** 2 EF | ABCD***** 5 ABC | DEF** 2 DE | ABCF* 1 CF | ABED** 2 ABD | ECF*** 3 ABF | CDE* 1 A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) AB C D F E 5 8 Exercise - 50%/Majority Rule Consensus Trees FG | ABCDE****** 6 BC | ADEFG****** 6 DE | ABCFG***** 5 ABC | DEFG***** 5 ADE | BCFG* 1 DFG | ABCE* 1 Split Frequencies Draw the 50%/Majority Rule consensus trees for these 6 trees Work again with the same table of split frequencies as for previous exercise Exercise - 50%/Majority Rule Consensus Trees FG | ABCDE****** 6 BC | ADEFG****** 6 DE | ABCFG***** 5 ABC | DEFG***** 5 ADE | BCFG* 1 DFG | ABCE* 1 Split Frequencies Draw the 50%/Majority Rule consensus trees for these 6 trees Work again with the same table of split frequencies as for previous exercise ? C ? C Majority Rule (Extended) Consensus Tree iiiiiiivvviviiviii AB | CDEF******** 8 CD | ABEF** 2 EF | ABCD***** 5 ABC | DEF** 2 DE | ABCF* 1 CF | ABED** 2 ABD | ECF*** 3 ABF | CDE* 1 A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) AB F E D C 5 8 3 Split Networks - Visualising Split Incompatibility A B C D E F (i) A B C D E F (ii) A B D E C F (vi) A B E D C F (vii) (iii) A B C D E F (v) A B D C E F A B F E C D (iv) A B D C E F (viii) 2 iiiiiiivvviviiviii AB | CDEF******** 8 CD | ABEF** 2 EF | ABCD***** 5 ABC | DEF** 2 DE | ABCF* 1 CF | ABED** 2 ABD | ECF*** 3 ABF | CDE* 1