Copyright (c) 2008 Daniel Huson. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation

Transcription

1 Daniel H. Huson and David Bryant Software Demo, ISMB, Detroit, June 27, 2005

2 Copyright (c) 2008 Daniel Huson. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license can be found at

3 SplitsTree4 is a program that for evolutionary analysis using trees and networks. Input: a set of taxa represented by characters, distances, quartets, trees or splits Output: trees or networks obtained using one of many different methods.

4 Written in Java, requires a JRE Installers are freely available from www. s p l i t s t r e e. o r g. sp l i t s t r e e_ l i nux_4be t a26. r pm (Linux) sp l i t s t r e e_un i x_4be t a26. sh (Linux & Unix) sp l i t s t r e e_un i x_4be t a26. sh sp l i t s t r e e_ma cos_4be t a26. s i t (MacOS) sp l i t s t r e e_w i ndows_4be t a26. e x e (Windows)

5 2 Splits networks 1 Phylogenetic trees 3 Reticulate networks Other types of phylogenetic networks Median networks from sequences Consensus (super) networks from trees Hybridization networks Special case: Galled trees Recombination networks Augmented trees Split decomposition, Neighbor-net from distances Ancestor recombination graphs Any graph representing evolutionary data

6 Represents incompatible signals in data, from: Sequences, e.g.: Median network (Bandelt et al 1994) Spectral analysis (Hendy and Penny 1993) Distances, e.g.: E.g. Split decomposition (Bandelt and Dress 1992) Neighbor-NetNet (Bryant and Moulton 2002) Trees, e.g.: Consensus network (Holland and Moulton 2003) Super network (H., Dezulian, Kloepper and Steel 2004) Bootstrap network (H., implemented in SplitsTree4)

7 Every edge of a tree defines a split of the taxon set X: x 6 x 1 x 4 x 8 e x 5 x 2 x 7 x 3 x 1,x 3,x 4,x 6,x 7 vs x 2,x 5,x 8

8 Tree T: Split encoding (T): 5 trivial splits: 2 non-trivial splits:

9 Two splits A 1 B 1 and A 2 B 2 of X are compatible,, if {A 1 A 2, A 1 B 2,B 1 A 2,B 1 A 2 } Two compatible splits: A 1 B 1 x 4 A 2 B 2 x 2 x 3 x 7 x 8 x 1 x 5 x 6 x 9 X

10 Two splits A 1 B 1 and A 2 B 2 of X are compatible,, if {A 1 A 2,A 1 B 2,B 1 A 2,B 1 A 2 } Two splits: A 1 B 1 x 4 x 5 A 2 B 2 x 6 x 2 x 1 x 7 x 3 X

11 Consider the following two trees T 1 and T 2, for which the splits are incompatible: T 1 + T 2 SN( ) The splits network SN( ) represents the incompatible set of splits := (T 1 ) (T 2 ), using bands of parallel edges for incompatible splits.

12 If characters have only 2 states and not too conflicting: interpret columns as splits and draw full splits network

13 Split decomposition or Neighbor-Net Net produces network from distances

14 A collection of trees can be represented by a consensus network or super network

15 Draw all splits that have positive bootstrap score

16 Compare the result of Split Decomposition with an NJ tree and bootstrap network: 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

17 Splits network can be rooted e.g. using an outgroup

18 Hybridization networks from gene trees trees [Huson, Kloepper, Lockhart and Steel, RECOMB 2005] Recombination networks from binary sequences [Huson and Kloepper, ECCB 2005]

19 Input trees all splits Reticulate network that induces all input trees

20 : : : : : : b : r : c : d : o : outgroup root

21 Input: Restriction maps of the rdna cistron (length 10kb) of twelve species of mosquitoes using eight 6bp recognition restriction enzymes [Kumar et al,, 1998]: Aede s a l bop i c t us Aede s a egyp t i Aede s s e a t o i Aede s a vop i c t us Aede s a l c a s i d i Aede s k a t he r i nens i s Aede s po l yne s i ens i s Aede s t r i s e r i a t us Aede s a t r opa l pus Aede s epa c t i us Ha emagogus equ i nus A r m i ge r e s suba l ba t us Cu l e x p i p i ens T r i p t e r o i de s bambus a Sabe t he s c y aneus Anophe l e s a l b i manus s

22 This data set was analyzed using different tree- reconstruction methods with inconclusive results. The associated splits network (or median network [Bandelt in this context), with edges labeled by the corresponding mutations: Anopheles_albimanus [Bandelt et al,, 1995] root 10 Aedes_katherinensis Aedes_seatoi Aedes_alcasidi Aedes_flavopictus Aedes_albopictus 25 Aedes_polynesiensis 3,5,9,14-15,21, Tripteroides_bambusa ,23,26 Aedes_aegypti Sabethes_cyaneus 13 Culex_pipiens 19 Haemagogus_equinus Aedes_triseriatus Aedes_epactius Aedes_atropalpus Armigeres_subalbatus

23 Recombination scenarios based on the complete data set look unconvincing. However, trial-and-error removal of two taxa Aedes triseriatus and Armigeres subalbatus gives rise to a simpler splits network: Anopheles albimanus root 3,5,9,14-15,21,24 11 Sabethes cyaneus Aedes katherinensis Aedes seatoi Aedes alcasidi 13 Haemagogus equinus Aedes polynesiensis Aedes aegypti Aedes albopictus Aedes flavopictus Aedes epactius Aedes atropalpus 17,23,26 Culex pipiens Tripteroides bambusa

24 A possible recombination scenario is given by: Anopheles_albimanus root 3,5,9,14-15,21,24 Sabethes_cyaneus ,25 2 Haemagogus_equinus 7 19 Aedes_aegypti 17,23,26 Aedes_epactius Aedes_atropalpus Culex_pipiens Tripteroides_bambusa Aedes_polynesiensis Aedes_katherinensis Aedes_seatoi Aedes_alcasidi Aedes_albopictus Aedes_flavopictus Here, Haemagogus equinus appears to arise by a single- crossover recombination, and a second such recombination leads to A.albopictus and A.avopictus.

25 Assumptions Taxa Taxa are represented e.g. by aligned sequences Unaligned Characters Bootstrap Transform characters into distances e.g. using Hamming Transform distances splits in Transform to network e.g. using Every connector distances into splits the equal angle represents a e.g. data using Neighbor- algorithm transformation net (plug-in) Distances Quartets Trees Splits Network

26 Taxa: the names of all taxa. Unaligned: unaligned sequences. Characters: aligned character sequences. Distances: pairwise distances between taxa. Quartets: (possibly weighted) quartet topologies. Trees: list of (possibly partial) trees. Splits: (possibly weighted) splits. Network: phylogenetic tree or network. ST_Assumptions: contains all methods and options used to compute data. ST_Bootstrap: bootstrap support of splits.

27 SplitsTree can read and write the following phylogeny formats: NEXUS, FastA, Phylip, ClustalW SplitsTree can produce the following graphics formats: GIF, JPEG and PNG (pixel formats) PostScript and SVG (vector formats)

28 4beta26: User manual now available from