1.0 User's Guide - Taxonomy and Systematics at Glasgow
Contents
1. Open c development bcd gene tree examples maddison ms Current gene trees mapped on to 166 random trees Seed 754997756 trees generated using Yule model Histogram woo oo On e 00 Re 1 Summary statistics ni 1466 mean 5 3956 sd 2 192 mini E max J Humber obs 1115 34 The Log window displays the results of your analyses The status bar at the bottom of the window displays the number of bytes in the buffer and how full the buffer is Currently the buffer is limited to 32K and will not store any information when that limit is reached You can use the Clear command on the Edit menu to clear the Log window buffer The contents of the Log window can be saved to a text file using the Save as text command and they can be copied to the Clipboard using the Copy command GENETREE User s Guide 12 3 6 2 Text editor GENETREE has a simple text editor that can be used to create and edit data files In addition to standard editing features such as copying and pasting text from the Clipboard and search and replace functions the editor also enables you to edit tree descriptions in situ To do this e Select the tree description including the semicolon in the editor window BEGIN TREES Species tree s1 TREE Tl Mc AAA E ENDELOCE e Choose the Edit tree command or press Ctrl E Windows or E Macintosh The program will open the tree description in the tree editor e Once you ve ed2. Orthologous A pair of genes that are descendants of the same copy of a gene are orthologous Paralogous A pair of genes separated by at least one gene duplication are paralogous species 1 2 3 1 2 3 genes a b C d e f duplication Phylogeny for three species 1 3 and six a f genes that stem from a gene duplication resulting in two paralogous clades of genes and B The amp genes a c are orthologous with each other as are the B genes d f however any and any B gene is paralogous as they are separated by a gene duplication Reconciled tree The simplest embedding of an associate tree inside its host tree Sorting event The apparent absence of a gene in the descendants of a species which itself had that gene Sorting events include gene loss but may also simply reflect failure to detect a copy of the gene in a species Tanglegram A diagram showing a species and gene tree facing each other with pairs of species and genes linked GENETREE User s Guide 6 2 2 Reconciled trees The concept of reconciled trees dates from Goodman et al s 1979 attempts to reconcile disagreements between then accepted mammalian evolutionary relationships and those obtained from haemoglobin genes Largely neglected until recently reconciled trees are now receiving renewed attention from biologists and mathematicians Eulenstein et al 1997 Guig et al 1996 Mirkin et al 1995 Page and Charleston 1997a Page and Charleston 1997b Yuan et
3. GENETREE User s Guide 8 3 Using the program This section gives an overview of how to use GENETREE Topics covered include installation configuration file formats using the Bork BLAST server and more 3 1 Obtaining GENETREE GeneTree can be freely downloaded from the Internet by visiting http taxonomy zoology gla ac uk rod genetree genetree html The program is free but please register your copy by sending an email to r page bio gla ac uk This will enable me to keep you informed of bug fixes and updates 3 2 Installation 3 2 1 Mac OS The Macintosh version requires a Power Macintosh running System 7 5 or later and the free Internet Config system extension This extension stores information about your Internet preferences and applications and GENETREE uses it to communicate with your Web browser To install GENETREE simply double click the self extracting file genetreeppc sea You will need to install the font COMPONENT Monaco on your system To do this drag the COMPONENT Font File onto your System folder A COMPONENT Font File 3 2 2 Windows GENETREE is a 32 bit program that requires Windows 95 or NT 4 0 To install the program unzip the file genetree zip and run the installation program setup exe This program installs GENETREE on your computer and supports the Uninstall feature of Windows 95 NT so that you can remove GENETREE from your computer using the Add Remove Programs control panel application 3 3 In
4. Fitter default T E hofiter M Expect 10 Culos default strana both y Descriptions 50 y Alignments 50 Histogram Other advanced options Parsed HTMLIV 37339 Document Done This returns a page listing the sequences most similar to your query sequence in typical BLAST format The next step in the analysis is to select the sequences you wish to analyse further Once the sequences are selected clicking on either the Local Alignments or Global Alignments button starts the following analysis e the sequences are aligned using ClustalW e a neighbor joining tree is constructed for the aligned sequences e aspecies tree is constructed for the taxa the genes were obtained from using the current taxonomy of the species e areconciled tree is constructed for the gene and species trees The results of the analysis are displayed in a single Web page part of which appears below y Netscape GLOBAL ALIGNMENTS EVALUATED FROM BLAST2 SEARCH RESULT File Edit View Go Bookmarks Options Directory Window Help joa 2 Qela 0 Location http www bork embl heidelberg de Blast2e getalign_global htralitmultiple_alignment OPSI_ASTFA OPSH_CARAU OPSG_CARAU OPSG_CHICK Gecko gecko 0PSB_ANOCA Gallus gallus OPST ASTPA OPSH CARAL OPSG CARAU OPSG CHICK 2Gocko gcouko OPSB ANOCA Gallus pallus OPSB GECGE 2Anolis carolinensis x Your comment is highly appreciated Thanks 31339
5. Document Done If you save this page to disk as an HTML file you can import it into GENETREE using the Import BLAST HTML command on the Internet menu This procedure can be a bit fraught for the following reasons GENETREE User s Guide 11 e The HTML file may be missing some information for example the species from which a sequence was obtained e The species tree may be incorrect and or missing one or more taxa e The gene tree is not a fully resolved rooted tree Because of this GENETREE converts the HTML into a temporary NEXUS file which it displays in it s text editor You can edit the tree descriptions by selecting them using the cursor then choosing the command Edit tree from the Edit menu This opens the tree in a tree editor Once you ve edited the tree closing the tree editor replaces the original tree description with one corresponding to the edited tree To process the file chose the Execute command on the File menu If successful GENETREE will display the trees otherwise it will report an error and display its location in the edit window 3 6 User Interface The user interface to GeneTree includes a Log window to record results of analyses text edit windows and various tree and chart display windows Note that each window has it s own specific menu commands and that some commands are only available when the appropriate window is active 3 6 1 Log window GeneTree co 1996 Roderic DO M Page
6. E EE E Riosa 9 ASS AT LO ee A a Cena St SPER RTCE ee oem 9 SF OWN TER NED ACCES dalla 9 EPEE TORMA rt dansa 9 30 GETTING DATA TROMTO ELN TERNERA tico 10 Sd USING INE DOT BLAST SC is da 10 SO SER INTERE ACE ai iS ni aaa 12 SOLLO WUD A A tigi E agate ica ant ate ae ta aed eI oa tT RE 12 SOL DENCIA A O AS E E 13 OSMA ION A a cados 13 LOA Reconciled WEE WINTLOWS rE E A IA 14 3 0 9 GraODMICALOULDUT a A A T 14 DOO PICO CONO A E A O A O E aa 14 IR aA IS 14 4 COMPARING GENE AND SPECIES TREES ccccssccscccccccccsccscccsccscceccescsccceccescssccscees 15 OPTIMALLY CRU RIA oiia a A Oe Ten On 15 AL UU OUUG OIL OUSSONG TOSCA AAA e 15 AL DUP UCAHONSHORIY AAA AA N 15 A DEE COVES CON CES AAA A A A ds Lo SPECIES PRED COS ura debia 16 ES RANDOM TREES cadie E da 16 ie URISTIC SEARCH stil titi lant O onana A n 16 ET ISU II UIE PT CC Sas at atest ten tases stn A RAT OAT OS ade MGA RS 17 AZ VECO DOT LON EA A e Was 17 ARS CONSTA A A A ns 17 AAA VECO SONG O EE EEE EE N omni caneenices 17 4 4 5 Deciding when to accept an improvement ocooocnnocnnnncnnonnnnnonnononnnnnnononnnnonononnnnonnnnononannnnononinnnns 17 LA OREU S A E E E 18 4 4 7 Excluding blocks from the AanalySTS ooooooccconcnnonnnonnnnnnnnnnnnnononnnnonononnnnononornnncnnnnnnononnnnnnnncnnons 18 ES HOW SPECIES RED COS is a at o la o e La at 18 EOS HOW GENE TRE COS St dd titles 18 AT PRIN SPECIES TREES Sloan loo O lalo CULO cio ola ela iO 18 AS SAVE SPECIES REE ele ete olen 19 A OWS
7. INC ONS UR AUNT dde 19 AO SHOW CONSTRATNT a sd sated Na els ee nical hia corns 19 REFERENCES cc 20 6 APRENDICES aiii 21 6 1 ACCESSING YOUR WEB BROWSER FROM WITHIN GENETREE ooccooccnccnnccnnccnncnnncnnncnnncnnnonononnnonnronnoos 21 OL WG OW SD SAIN TA A AA A oa 21 GENETREE User s Guide 3 6 1 2 Mac OS A A A AN AS A pata ee tater ca Han Sn led ee ataat 21 O REED aen A A A E E NE ee Sere ee err AET 22 Oz TSI LS TOON SN A teat Peele a 22 0 222 ONG OM a ee Manipula O A bie E 23 6 3 GENEL REE AND COMPONENT Ue e 24 GENETREE User s Guide 4 1 Preface GENETREE has its origins as part of my tree comparison program COMPONENT Page 1993 written while I was a post doc at the Natural History Museum in London However the code has been completely rewritten in C using Borland C and Metrowerks CodeWarrior and has been ported to the Macintosh Writing the cross platform interface to the program was made easier by using ideas from the National Center for Biotechnology s VIBRANT library written by Jonathon Kans and Julian Smart s wxWin C library Implementing tabbed dialog boxes and other features was made easier by public domain code from Jim Stout Jim s CDEFs and Gilles Vollant MRU library The installation program for Windows 95 NT comes courtesy of InstallShield Corporation The original impetus for writing GENETREE came from work by Joe Slowinski and Boris Mirkin The algorithm for constructing a reconciled tree is described in
8. Page 1994 The heuristic search strategy was influenced by many discussions with Mike Charleston Charleston 1995 and the program uses Oliver Eulenstein s upublished algorithm for computing the cost of mapping a gene tree onto a species in linear time 1 1 Contacting the author Roderic D M Page Division of Environmental and Evolutionary Biology Institute of Biomedical and Life Sciences University of Glasgow Glasgow G12 8QQ Scotland United Kingdom Telephone 0141 330 4778 Fax 0141 330 5971 Email r page bio gla ac uk GENETREE User s Guide 5 2 Introduction GENETREE is an experimental tool for visualising and analysing the relationship between gene and species trees using reconciled trees If you are interested in using GENETREE I strongly suggest that you read the papers by Page and Charleston 1997a 1997b which describe the concepts behind the program Preprints of these papers can be downloaded from my Web site http taxonomy zoology gla ac uk rod pubs html A quick overview of reconciled trees is provided below 2 1 Terminology Some terminology used in this manual is defined below Duplication May literally be a gene duplication resulting in paralogous copies of the gene but is also used here to describe cladogenesis of genes independent of speciation such that a species has more than one copy of the gene Hence duplication is also used here to describe interspecific coalescence of alleles
9. we could chose to either a wait until all perturbations have been made and use the best tree found as the start of the next round of perturbations or b immediately restart the search using the better tree Option a means that we will always be using the best possible tree as the starting point for the search at the cost of the time to perform all rearrangements on each tree whereas option b will almost always be quicker to start a new round of perturbations the first tree to show an improvement is accepted although an even better tree may have been obtained had we waited Option a is in effect when the Steepest ascent check box is ticked otherwise option b is employed GENETREE User s Guide 17 4 4 6 Results The species trees found by heuristic search replace those already in memory for example those read in from the data file You can save the species trees to a NEXUS tree file using the Save Species Trees command 4 4 7 Excluding blocks from the analysis If you have more than one set of genes 1 e more than one DISTRIBUTION block then you may wish to analyse some of the genes separately By default all the Analysis menu commands operate on all the genes together You can change this by using the Include Exclude command By moving associates between the Include and Exclude lists you can specify which associates GENETREE uses when computing the total cost 4 5 Show species tree costs For each species tree This c
10. GENETREE 1 0 A program for comparing gene and species phylogenies on computers running Mac OS or Microsoft Windows 95 NT User s Guide by Roderic D M Page University of Glasgow Permission to use and distribute this software and its documentation for any purpose is hereby granted without fee provided the above copyright notice author statement and this permission notice appear in all copies of this software and related documentation THE SOFTWARE IS PROVIDED AS IS AND WITHOUT WARRANTY OF ANY KIND EXPRESS IMPLIED OR OTHERWISE INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHALL THE AUTHOR THE DIVISION OF ENVIRONMENAL AND EVOLUTIONARY BIOLOGY OR THE UNIVERSITY OF GLASGOW BE LIABLE FOR ANY SPECIAL INCIDENTAL INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE AND ON ANY THEORY OF LIABILITY ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE GENETREE User s Guide 2 Contents Naor crac 5 LT CON TA CTING THE AUTHOR iio 5 ZINT TRODUC TION ie a a a O e ease neue EE 6 2 LERMINOLOGY raer i E EE e a a 6 Dt INEC ONGIEED TRES sica 7 22d SCATCHING Jor OCPUMALSPCCICS TICS AAA AA AAA A AA 7 MSS RES R A A AA SS USITNG THE PROGRAM oe 9 3 POBTANING OENE LREE VS A NA ii 9 S INSTALLATION APRA dy ERRORS 9 SLA MACOS E A
11. IL 1a between gene and _ J aaan jae ene losses gt 9 ap aR trees Bovine Bovine IL b Sheep Sheep IL 1b AER Human Human IL 1b gene duplication Human Human IL 1bm required due to multiple Lado copies of gene in same Mouse Mouse IL 1b species Human Human IL 1ra Rat Rat IL 1ra Mouse Mouse IL 1ra del 14 44 10 1 de 16 Z cost of this reconciled tree The cost of the reconciled tree is displayed in the status bar in the form d l c xd yl dc c2 where cl is the sum of the number of duplications x and losses y and c2 is the number of deep coalescences Hence d 1 14 4d 101 dc 16 means that the reconciled tree requires four geen duplications and ten gene losses for a total cost of 14 and requires 16 deep coalescences If the DISTRIBUTION block contains a TITLE command then that text will appear in the title bar of the window You can change the window title by using the Rename command Note that if you have more than one gene tree in a DISTRIBUTION block the reconciled tree is computed for the gene tree that is currently displayed in the tanglegram window To change the gene tree select the desired tree from the popup menu in the tanglegram window 3 6 5 Graphical output The tree s displayed in the tanglegram and reconciled tree windows in GENETREE can be printed copied to the Clipboard or saved as a graphics file TO DO printing big reconciled trees 3 6 6 Tree editor GENETREE has a built in t
12. al in press Suppose we have a phylogeny for four species and four genes sampled from those species and that the two trees which we believe to be correct disagree a a organism gene 1 a 2 b 3 e 4 d The question is how can the trees both be true and yet be discordant One explanation is to embed the gene tree in the species tree b which requires us to postulate a number of gene duplications and subsequent losses in this instance one duplication and three losses This embedding can also be represented using a reconciled tree c which simply takes the embedded gene tree and unfolds it so that it lies flat on the page The reconciled tree would depict the complete history of the gene if there had been no gene losses the three sorting events As a consequence of the gene duplication we would expect species 2 3 and 4 to each have two copies of the gene That they do not requires us to postulate three gene losses Alternatively the gene copies may be present but undetected Hence the reconciled tree makes predictions about the existence of undiscovered genes It also suggests that genes b and c are paralogous to gene d which 1s not apparent from the gene phylogeny alone b c missing genes a b c a b d 1 2 3 4 sorting events reconciled tree 2 2 1 Searching for optimal species trees Reconciled trees can be used to find the best species tree for more than one gene Given n gene t
13. cation ENDBLOCK At present all trees must be rooted and binary fully resolved 3 5 Getting data from the Internet As well as reading NEXUS files GENETREE can read HTML files produced by the Bork group s advanced BLAST server This server http www bork embl heidelberg de Blast2e automates analysis of a set of sequences using reconciled trees The server is experimental but its output can be a useful starting point for further analysis 3 5 1 Using the Bork BLAST server From within GENETREE you can go to the Bork BLAST server using the Bork BLAST server command on the Internet menu Full details on using the Bork BLAST server are given in Yuan et al in press and in documentation at the site itself The first step in the analysis is to paste in a query sequence and click on Submit Query GENETREE User s Guide 10 ea Netscape Bork Group s BLAST2 amp Orthologue Search Service at EMBL Fie Edit View Go Bookmarks Options Directory Window Help slo al 2 z Bla 0 2 Location http www bork embl heidelberg de Blast2e v Advanced BLAST2 amp Orthologue Search with post processing Sas NEW Finding rthologues amp Distinguishing them from paralogues in databases HELP Choose program and database to use for your search Program blastp Database hrab Enter here your sequence in FASTA or raw format Submit Query Clear Options for the BLAST server Matrix BLOSUME2 T
14. commands set the optimality criterion used for scoring reconciled trees 4 1 1 Duplications and losses The default optimality criterion is the number of duplications and losses required to reconcile the gene tree with the species tree 4 1 2 Duplications only Choosing this criterion means that the number of gene losses is ignored This may be appropriate if the sampling of different taxa is uneven Page and Charleston 1997a 4 1 3 Deep coalescences Counting duplications and losses is appropriate if gene duplication is the cause of multiple gene lineages However at lower taxonomic levels multiple sequences may be alleles rather than paralogus loci GENETREE uses Maddison s Maddison 1997 concept of deep coalescence as a criterion of fit between allele phylogenies and species trees In the figure below alleles c and d coexist in the common ancestor of species 3 and 4 but do not coalesce until we go down the tree to the common ancestor of species 2 3 and 4 This failure of two allele lineages to coalesce in the species lineage in which they first co occur counts as a single deep coalescence event and hence the cost of the reconciled tree is 1 deep coalescence organism GENETREE User s Guide 15 GENETREE computes the deep coalescence cost of a reconciled tree by counting the number of gene lineages that do not coalesce on each branch of the species tree 4 2 Species tree cost The Species Trees command allows you to c
15. do a change and recover the old tree by choosing Undo from the Edit menu or by using these keys Z MacOS Ctrl Z Windows Choosing the Undo command again restores the tree you just undid Undo is only available for the operations that materially affect the tree topology move branch collapse branch collapse clade and reroot Cosmetic changes such as rotate branches cannot be undone The Undo menu item will reflect which type of move can be undone for example the menu item will read Undo move branch if you are using the move branch tool GENETREE User s Guide 23 6 3 GeneTree and COMPONENT 2 0 This is intended for users of COMPONENT 2 0 Page 1993 Several commands in the Map trees submenu in COMPONENT have exact equivalents in GeneTree These are listed below COMPONENT command GENETREE equivalent Reconcile with tree GENETREE automatically displays the reconciled tree Map onto all trees Species tree fit Options GENETREE always treats species without genes as missing information Heuristic search Heuristic search Some features of COMPONENT are not in GENETREE These include the ability to arbitrarily resolve polytomies in input trees and the Prune each leaf command GENETREE User s Guide 24
16. e R D M 1993 COMPONENT Tree comparison software for Microsoft Windows Version 2 0 The Natural History Museum London Page R D M 1994 Maps between trees and cladistic analysis of historical associations among genes organisms and areas Syst Biol 43 58 77 Page R D M and Charleston M A 1997a From gene to organismal phylogeny reconciled trees and the gene tree species tree problem Mol Phylog Evol 7 231 240 Page R D M and Charleston M A 1997b Reconciled trees and incongruent gene and species trees In Mathematical Hierarchies in Biology B Mirkin F R McMorris F S Roberts and A Rzhetsky Eds Vol 37 pp 57 70 American Mathematical Society Providence Rhode Island Swofford D L and Olsen G J 1990 Phylogeny reconstruction In Molecular systematics D M Hillis and C Moritz Eds pp 411 501 Sinauer Associates Sunderland Yuan Y P Eulenstein O Vingron M and Bork P in press Towards detection of orthologues in sequence databases Comput Applic Biosci GENETREE User s Guide 20 6 Appendices 6 1 Accessing your Web browser from within GENETREE The online help and Bork server access features of GENETREE require that GENETREE can locate and talk to your Web browser program 6 1 1 Windows95 NT 4 0 Under Windows 95 NT 4 0 this should be automatic GENETREE uses the Windows registry to locate the browser If this fails then it is possibl
17. e that the browser is not correctly installed If this is not the case contact me to resolve the problem 6 1 2 Mac OS You must have Internet Config installed and configured on your machine in order for GENETREE to be able to talk to your Web browser Internet Config is a freeware system extension that allows applications to share the same preferences You can add your e mail address news information and Helper configuration information into Internet Config once instead of in each of your Internet applications Applications that are Internet Config aware include Microsoft Internet Explorer among others You can download Internet Config 1 3 from most Mac OS software collections or from the Glasgow Taxonomy Server http taxonomy zoology gla ac uk rod treeview help InternetConfig 1 3 sea hqx Once you have Internet Config installed you need to ensure that your Web browser is listed as your http helper in Internet Config s settings To do this follow these steps 1 Click on the Helpers button in the Internet Preferences dialog Helpers 2 Inthe Helpers dialog box set the http helper to your browser by clicking the Add button Once you ve added your browser you should see something like this Helpers E p gopher Turbobopher http Netscape Navigator 2 01 L mailto Eudora GURL Handler a a 3 Quit Internet Config remembering to save your settings When you start GENETREE the program will u
18. egraft apr Alternate nni and spr Ge F Ernane constant MV Retain trees of equal cost e Steepest ascent GENETREE User s Guide 16 4 4 1 Starting trees The search can either start from the current species tree or from one or more random trees the later is the default Typically a search should use a number of random starting points however there may be times that you want to explore the landscape around a species tree For example after doing a search without retaining equally good solutions you may wish to see whether more than one tree with that cost exists Random starting trees tend to be poor estimates of the optimal species tree but using multiple random trees gives information on the search landscape of the problem Charleston 1995 In particular convergence on the same cost value from multiple starting points suggest that that cost value may be optimal Multiple starting points also increase the chance of detecting multiple equally good solutions 4 4 2 Tree perturbation GENETREE offers three kinds of tree perturbations or branch Swofford and Olsen 1990 nearest neighbour interchanges nni subtree pruning and regrafting spr and alternate nni s and spr s Nni s offer quick but rather limited perturbation whereas spr is much more extensive and as a consequence more time consuming The alternate strategy alt combines both nni and spr by first trying nni s then if no nni produces an improvement
19. f any in the Log window GENETREE User s Guide 19 5 References Charleston M A 1995 Towards a characterization of landscapes of combinatorial optimisation problems with special reference to the phylogeny problem J Comput Biol 2 439 450 Constantinescu M and Sankoff D 1986 Tree enumeration modulo a consensus J Classif 3 349 356 Eulenstein O Mirkin B and Vingron M 1997 Comparison of annotating duplications tree mapping and copying as methods to compare gene trees with species trees Jn Mathematical Hierarchies in Biology B Mirkin F R McMorris F S Roberts and A Rzhetsky Eds Vol 37 pp 71 93 American Mathematical Society Providence Rhode Island Goodman M Czelusniak J Moore G W Romero Herrera A E and Matsuda G 1979 Fitting the gene lineage into its species lineage a parsimony strategy illustrated by cladograms constructed from globin sequences Syst Zool 28 132 168 Guig R Muchnik I and Smith T F 1996 Reconstruction of ancient molecular phylogeny Mol Phylog Evol 6 189 213 Maddison D R Swofford D L and Maddision W P 1997 NEXUS An extensible file format for systematic information Syst Biol 46 590 621 Maddison W P 1997 Gene trees in species trees Syst Biol 46 523 536 Mirkin B Muchnik I and Smith T F 1995 A biologically consistent model for comparing molecular phylogenies J Comput Biol 2 493 507 Pag
20. ited the tree close the tree editor You will be prompted to save the tree AN Tree null has been modified Do you want to save these changes e If you click on the Yes button the tree description highlighted in the editor window will be replaced with the tree description corresponding to the edited tree 3 6 3 Main window The main window displays a tanglegram showing the host tree and an associate tree If you have more than one associate block you can change the block displayed in the tanglegram by making the corresponding block window active The tanglegram window displays the total cost of all the reconciled trees in the active blocks If you have more than one host or associate tree you can select alternative trees to display using the popup menus in the tool bar fy Mammal interleukins nex Iof ES Host tree E gt Associate tree T Rabbit IL 1a Human IL 1 bm Human IL 1ra Mouse IL 1ra Rat IL 1ra GENETREE User s Guide 13 3 6 4 Reconciled tree windows Each DISTRIBUTION block has a corresponding window which displays the reconciled tree for the current gene tree in that block and the current species tree toggle display of reconciled tree or the gene tree species gene obtained from name of gene Interleukine 1 OF ES Siz Ys Rabbit Rabbit IL 1a Human Human IL 1a ati Pi Pig IL 1a gene duplication Bovine Bovine IL 1a inferred from mismatch Ra Rat IL 1a Mouse Mouse
21. ommand shows the cost of reconciling the current gene tree for current DISTRIBUTION block gene with all the species trees All the optimality criteria duplications losses and deep coalescence are computed Species tree or gal de 1 0 0 0 2 173 1 3 173 1 4 LAS 1 5 1 4 2 6 1 4 2 7 2 7 3 8 24 4 3 9 2 7 3 10 2 7 3 11 2 7 3 12 2 7 3 13 1 3 1 14 2 6 2 15 2 6 2 d l duplications and losses dc deep coalescences 4 6 Show gene tree costs This command shows the cost of reconciling the current gene tree for each DISTRIBUTION block with the current species tree All the optimality criteria duplications losses and deep coalescences are computed 4 7 Print species trees GENETREE User s Guide 18 Prints the species trees You can print more than one tree per page 4 8 Save species trees Saves the species trees to a NEXUS format tree file 4 9 Edit constraint Opens the tree editor see Appendix and displays the current constraint tree If you have not defined a constraint tree the current species tree will be used By editing this tree you can prevent the heuristic search from considering certain trees For example the tree below constrains the heuristic search to consider only species trees that have mammals birds amniotes and eukaryotes as clades 4 10 Show constraint Bacteria Barley Fundulus Lamprey Telost Shark Duck Chicken Human Rat Mouse Rabbit Pig Cow Displays the current constraint tree i
22. ompute the total cost of all species trees when reconciled with the current gene tree in each active DISTRIBUTION block The resulting distribution is displayed in a chart window The cost computed depends on which optimality criterion you have selected see previous section 4 3 Random trees The Random Species Trees command allows you to compute the total cost for a set of random species trees The current gene tree in each active DISTRIBUTION block is reconciled with each random species tree and the resulting distribution of total cost is displayed in a chart window The cost computed depends on which optimality criterion you have selected see previous section 4 4 Heuristic search One use of GENETREE is to find the species tree that the gene trees best fit 1 e the species tree with the smallest total cost when reconciled with all gene trees This tree is most parsimonious in the sense of minimising the total number of events required to explain the evolutionary history of the genes The problem of finding the optimal species tree is NP complete so GENETREE uses a heuristic approach There are a number of options available which affect how the search is undertaken and these are set in the Heuristic search dialog box Heuristic search Ea Starting tree Cancel dl Random tee Number of searches i ae t System clock C User value fo Tree perturbation C Nearest neighbour interchange rni C Subtree prune and r
23. ree editor which can be used to edit tree descriptions in NEXUS text files as well as construct constraint trees The editor 1s described in more detail in the Appendices 3 6 7 Online help You can access the GENETREE online help through your Web browser using the Help command On the Macintosh this command appears under the za menu in Windows it appears on the Help menu Chosing this command will launch your Web browser and display the help pages for GENETREE This command requires that you have a properly configured Web browser and an Internet connection on your machine see the Appendix for more details The Macintosh version of the program also supports Balloon Help GENETREE User s Guide 14 4 Comparing gene and species trees GENETREE computes the cost between one or more gene trees and a species tree that you have supplied or inferred using the program The cost for each gene is displayed in the corresponding reconciled tree window The total cost is displayed in the tanglegram window Using the Analysis menu commands you can perform a range of further analyses You can select the optimality criterion for scoring reconciled trees compute the total cost of all species trees compute the total cost for a set of random species trees perform a heuristic search for the species tree or trees that yield the lowest cost save any species trees you have computed construct constraint trees 4 1 Optimality criteria The first three
24. rees G G G and species tree T the cost of reconciling all n gene trees is simply the sum of the costs of reconciling the individual gene trees c G 7 c G T c G T An analogy that may be helpful when using GENETREE is to think of each gene as a character each terminal sequence GENETREE User s Guide 7 as a character state and the gene tree is the character state tree Mapping the gene tree onto the species tree 1s equivalent to optimising a character on a tree The cost of the reconciled tree is equivalent to the length or number of steps a character requires 2 2 2 Missing genes If we are comparing more than one gene tree with a species tree then it will often be the case that not all the genes are known in all the species of interest While the algorithms for mapping two trees and for constructing the reconciled tree are still applicable in this case the number of losses computed needs to be interpreted carefully For example in the algorithm described above a gene tree for four genes may be perfectly consistent with a larger species tree on n gt 4 species say but the lack of genes in the remaining n 4 of those species will be counted as losses Given the uneven taxonomic sampling in the sequence data bases a more reasonable interpretation may be that these species simply have not been sequenced for that gene This is the approach adopted in GENETREE For more details see Page and Charleston 1997a 1997b
25. se Internet Config s settings to locate your Web browser and will communicate with your browser via the Internet Config extension GENETREE User s Guide 21 6 2 Tree Editor The tree editor provides tools for moving branches rerooting polytomy formation and rearranging the appearance of the tree The tools available are displayed in the tool bar Tree Editor PAUP_1 To select a tool click on the icon corresponding to the tool you want to use Once you have selected a tool the cursor will change to the appropriate shape To manipulate the tree click the cursor on a branch the corresponding operation will be performed on that branch unless the desired operation is invalid in which case the tree editor gently beeps and ignores the command The default tool is the arrow tool which is used for moving branches 6 2 1 Using the tools Move branch A branch can be picked up and moved to another part of the tree by clicking on the branch and dragging it to the new position The branch being moved will be highlighted with a different colour and the cursor will change from an arrow to a small diamond Tapaculo a Flicker ra Pitta Canastero Drag the diamond cursor to the position you want to move the branch and release the mouse button If the new placement is invalid for example moving a branch onto one of its descendants the tree editor will gently beep and ignore your request Pa Collapse branch Clicking wi
26. sprs are tried In practice a single run if nni s from a random starting tree is not very effective although multiple runs may encounter the optimal solution Spr tends to be time consuming but effective Alt tends to be quicker than spr and as effective Page and Charleston 1997a and hence is the default 4 4 3 Constraints In some cases it may be unnecessary to search the space of all possible species trees For example if we assume that mammals are monophyletic then species trees in which mammals do not form a clade can be safely ignored GENETREE uses a constraint tree Constantinescu and Sankoff 1986 to represent the set of possible species trees If you create a constraint tree and check the Enforce constraint check box then GENETREE will only consider species trees that are compatible with the constraint tree 4 4 4 Tree storage You can elect to store all the species trees of equal cost that are found by GENETREE up to the program s limit of or just one If you chose the former by ticking the Retain trees of equal cost check box and GENETREE finds more than one tree each tree in turn will act as the starting tree for a heuristic search 4 4 5 Deciding when to accept an improvement GENETREE takes a tree and starts to perturb that tree in search of a better tree If a better tree is found the search begins again using the better tree until no perturbation produces an improvement If a perturbation produces an improvement
27. ternet access Some GENETREE features require access to the Internet If properly configured GENETREE can communicate directly with your Web browser See the Appendices for details about configuring Internet access 3 4 File format GENETREE uses essentially the same variant of the NEXUS format Maddison et al 1997 used by COMPONENT 2 0 Page 1993 The input file comprises a TAXA block one or more DISTRIBUTION blocks and a TREES block unlike COMPONENT the TREES block must be included You are referred to the COMPONENT manual or that program s online help for details The basic syntax is GENETREE User s Guide 9 NEXUS species names BEGIN TAXA DIMENSIONS NTAX number of species TAXLABELS speciesl Species2 ENDBLOCK Gene tree s BEGIN DISTRIBUTION TITLE title string NTAX number of sequences For each gene sequence list the species it comes from RANGE Sequence_1 species_x sequence_2 species_x sequence_ntax species_x one or more trees for these sequences TREE tree name rooted tree specification TREE tree name rooted tree specification ENDBLOCK Additional DISTRIBUTION blocks may go here Optional constraint on species tree BEGIN ASSUMPTIONS CONSTRAINT constraint name rooted tree specification ENDBLOCK species tree descriptions go here BEGIN TREES TREE tree name rooted tree specification TREE tree name rooted tree specifi
28. th this tool on an internal branch deletes that branch produces a polytomy The editor ignores attempts to delete terminal branches Collapse clade Clicking with this tool on an internal branch collapses the clade above that branch Reroot Clicking on a branch with this tool reroots the tree on that branch The next four tools change the appearance of the tree in the window but do not affect the cladistic topology They cannot be undone GENETREE User s Guide 22 Rotate branches This tool rotates the descendants of a binary node so that the left descendant is now the right descendant and visa versa You can only use this tool on binary internal nodes If you want to rearrange the descendants of a polytomy you must use the next tool Exchange branches To rearrange the order of the descendants of a polytomy use this tool to interchange pairs of branches Click on one descendant drag the cursor onto the other descendant and release the mouse button Ladderize left This tool orders the subtree rooted at the branch clicked on so that the heavier nodes those nodes with the largest clusters appear leftmost uppermost on the screen Ladderize right This tool orders the subtree rooted at the branch clicked on so that the heavier nodes those nodes with the largest clusters appear rightmost lowermost on the screen 6 2 2 Undoing a tree manipulation The tree editor remembers the previous tree so that you can un
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