Allan Wilson

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Allan Wilson Centre An introduction to trees An introduction to trees and and networks networks David Penny Allan Wilson Centre for Molecular Ecology and Evolution overview of talk trees and networks (with cycles) spanning and phylogenetic (Steiner) trees exploratory data analysis, visualization multiscale splits compatibility/incompatibility application - the MinMax squeeze overview tree terminology .. . . 1d 6.3 4 3.7 5 3.5 5.5 6 6.1 5.9 1a 1b . .. 1e n . . . p q o 1c m r s 1f t1 t2 t3 t4 t5 t6 t5 1g 1h t1 1i t4 t1 t2 t3 t4 t5 t6 t1 t2 t3 t4 t5 t6 t2 t6 t3 1c, spanning tree 1f, phylogenetic (Steiner) tree multiscale, popn growth lose internal nodes 0 1 2 3 lose nodes near the root mixture of spanning and Steiner trees minimum spanning subtrees even using complete sequences the question of multiscale effects of time scale sequences abundant ancestral states still present multifurcations and cycles sites in same rate class (gamma) neutral plus deleterious sequences sparse speciation only at tips binary phylogenetic trees sites on or off, covarion model average over all sites hypervariable sites TIME SCALE generations populations species families orders classes phyla microevolution macroevolution dataset used to argue poor Data set against RASA RASA performance of Mol. Biol. Evol. 19:14–23. 2002 RASA1.NXS taxon A taxon B taxon C taxon D taxon E taxon F taxon G taxon H taxon I taxon J 1000010000 1000001000 0100001000 0100000100 0010000100 0010000010 0001000010 0001000001 0000100001 0000110000 taxonH taxonG taxonI taxonF taxonJ taxonE taxonA taxonD taxonB 0.01 Fit=100.0 ntax=10 nchar=10 -dsplits -hamming taxonC some reasons for cycles? repeated mutations – random (insufficient information) - systematic [e.g. GC bias] - positive selection hybridization gene conversion/concerted evolution lateral transfer (incl. endosymbiosis) alternative (non-Steiner tree) models (incorrect assumptions about the mechanism) exploratory data analysis - EDA pika rabbit guineapig canerat strict consensus tree aardvark treeshrew tenrec dormouse squirrel rat mouse vole elephant armadillo loris cebus flyingfox mole harbseal cat whiterhino horse cow pig gibbon fruitbat baboon macaca dog human hippo finwhale rabbit pika guineapig canerat dormouse aardvark tenrec 10% consensus treeshrew elephant armadillo squirrel harbseal dog cat vole rat mouse horse whiterhino pig mole loris cebus cow fruitbat flyingfox human gibbon finwhale hippo macaca baboon rabbit pika guineapig canerat bandicoot opposum wallaroo possum treeshrew dormouse squirrel aardvark tenrec elephant platypus cebus human gibbon armadillo loris baboon macaca harbseal dog cat mole fruitbat flyingfox horse whiterhino pig cow finwhale hippo consensus methods lose information taxon taxon taxon taxon A B C D 1 1000 0100 0010 0001 2 110 101 011 000 3 1000 0111 0100 0010 Three data sets from Bandelt et al (1995). The consensus of each would be a polytomy as for (a). However, the median network of each shows that each has a different data structure 000 1000 0100 1000 0010 0010 0001 110 101 011 0100 0111 are sites always in the same rate class? observed NJ LowG+C cyanobacteria HighG+C 100 100 87 expected under i.i.d Split graph/dcov LowG+C HighG+C cyanobacteria observed Split graph/dcov LowG+C HighG+C cyanobacteria green plants green plants. green plants. 100 98 82 γ α γ α γ α AtpB Similar results for RecA, 16SrDNA, Hsp60, FtsZ (2000) MBE 17, 835-838 0.12 0.1 0.08 0.06 0.04 0.02 0 -0.02 -0.04 -0.06 Lento plot, ex Kerryn support clashes * * * * * * * * * * *++++++ ++ 50 40 30 20 10 0 -10 falcon & stork/penguin signals, Kerry’s birds 40 30 20 10 0 -10 -20 196 187 50 chicken & duck/goose 1 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 1 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 S1 overview of talk trees and networks (with cycles) spanning and phylogenetic (Steiner) trees exploratory data analysis, visualization multiscale splits compatibility/incompatibility application - the MinMax squeeze overview (contd) when MP and ML are equivalent Ø for a single column of data (this leads to), Ø there is no common mechanism shared by the characters, Ø maximum evolutionary pathway likelihood(ML ep) is equivalent to maximum parsimony, Ø there are effectively infinite character states (the same mutation never occurs twice) Ø abundant sequences? overview of talk trees and networks (with cycles) spanning and phylogenetic (Steiner) trees exploratory data analysis, visualization multiscale splits compatibility/incompatibility application - the MinMax squeeze overview 0.01 0.005 0.002 loss of information 1 0.8 0.6 0.4 0.2 0 1 -0.2 10 100 1000 0.001 10000 splits Ø from trees and networks Ø from data - sequences (character states) Ø from data - distances what is a split - from trees c b a d A B e what is a split - from trees c b a d A A = {a,b} B B = {c, d, e} e Denote by A | B. splits in a network c b a { a,b,c} {d,e} { a,b,e} {c,d} d e summary of introduction overview of talk trees and networks (with cycles) spanning and phylogenetic (Steiner) trees exploratory data analysis, visualization multiscale – generations to macroevolution splits – from trees, characters or distances compatibility/incompatibility application - the MinMax squeeze

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