A Rough Guide to S
Contents
1. 7 11 AC 40 35088 BC 40 35088 ABC 19 29824 optimal reconstruction number 1 S DIVA Value 368 4546 Analysis end at 2009 11 4 14 51 15 node 21 anc of terminals 7 11 AC 40 35088 BC 40 35088 ABC 19 29824 means gt Node 21 is the node of terminals 7 to 11 in the final tree gt The most recent common ancestor of terminals 7 to 11 had a range of AC or BC or ABC In our samples A means Africa B means Europe and C means China gt Yr F x of ancestor of terminals 7 to 11 originated in the AC is 40 35088 Support value of ancestor of terminals 7 to 11 originated in the BC is 40 35088 Support value of ancestor of terminals 7 to 11 originated in the ABC is 19 29824 In the final tree is the selected node The probability P of an ancestral range x at node n of the final tree is calculated as P x X1 F Xn i Pn where t is the selected tree m is the total number of sampled trees F x is the occurrence of an ancestral range x at node n for tree t The value x may represent a single area e g A or a widespread range e g ABC F x is calculated as the actual frequency of x within the pool of biogeographic pathways optimized using DIVA for each sampled tree Harris amp Xiang 2009 F x t The value i is the number of times the area x occurs in the total number of reconstructions at node n in tree t D optimal reconstruction number 1 S DIVA Value 368 4546 The statistical value S DIVA value SV of an op2. 7 6 8 9 10 11 replace with your tree lv A RECAEN distribution A A A AB B B B BC A ABC C replace with your distribution M Max areas at each node 44 Optimize Printrecs uit T Age E Weight 0 5 s M wold 1000 F Bouna 250 Estale a parilar node Run S DIVA only for a particular node You can specify a node using the following format I i seaside 1 2 3 4 50r 1 5 1 2 3 4 8 9 10 or 1 4 8 10 Numbers correspond to IDs in the jo timize Printrecs Maxareas 4 Weigh eyes 7 Distributions column in the S DIVA interface With an undefined sister x Specify a clade by the node shared with its sister and estimate the ancestral range of the clade and an undefined sister x Harris amp Xiang 2009 Specify the node using one of the formats shown above With omitted taxon distributed in Add distribution information for and topological placement of a taxon omitted from the phylogeny S DIVA manually places the unnamed taxon as sister to the specified node and considers its distribution when running the analysis Note The manually placed taxon is not included in graphical output Random tree Select random trees form trees data set to run the analysis Trees will be selected from between Burn in and Amount of trees You can save the randomly selected trees to a new file with File gt Save Processed Trees Hide detailed output Hide the output of analysis You can change this option while running Optimize Allow Reconst
3. B Species_05 2 A Species_02 A 0 99 the white space in the tree view 1 A Species_01 window 10 2000 Note that it is possible to make this too small for the width of the tree Distribution 3 A Species_03 4 AB Species_04 Show distribution 7 B Species_07 x Ejga areas These will display as red 0 99 6 B Species_06 letters next to the pie charts Color Pie Show colored pie chart Unchecking this will result in grayscale pie charts Support value Show support value for the node in the sample of trees Options for save picture analyzed i e pn Trans bg save the picture with transparent background If unchecked the picture will be saved with a white background File node of 1 11 The frequency of occurrence of this node in the loaded trees is 100 AC ABC BC ABC 71 89 BC 18 86 AC 9 25 Eg iolxi Zoom The measure of magnification of saved picture Mouse control Double click on a node Select the node Right click on a node Show or hide the pie chart Left click on a node Show the bar chart The left figure shows a result for estimating a particular node This can be accessed from from Graphic gt Node View 4 How to e e o back to contents In the compressed ZIP file download from here you will find a sample folder All sample files referenced in this manual are in the sample folder 4 1 How to make Trees data set 4 1 1 How to
4. DIVA but it is also not essential 1 Taxon_1 2 Taxon_2 3 Taxon_3 4Taxon_4 5 Taxon_5 6 Taxon_6 7 Taxon_7 8 Taxon_8 4 2 How to make a Final tree 9Taxon_9 10 Taxon_10 4 2 1 How to make a final tree by BEAST Back to Top tree 1 3 8 1 6 2 4 9 5 10 7 Launch TreeAnnotator exe ka B PFE k Set Burnin and Posterior Probability ree 3 3 41 tree 4 3 5 8 1 9 4 10 7 2 6 Choose your trees data set as Input Tree File tree 5 3 4 10 1 8 6 2 9 7 5 In our example we chose sample sample1 trees end Choose Output File We saved it as Sample1_Final_Tree tre in sample folder Sample1_Final_Tree tre is our final tree 4 2 2 How to make a final tree using PAUP Back to Top Define outgroups and root the trees with roottrees QOUTROOT MONOPHYL Export a tree using savetrees format NEXUS commands 4 2 3 How to obtain a final tree from other phylogenetic programs Back to Top If you are using Mrbayes you should make the final tree using BEAST or PAUP To make a final tree using other phylogenetic programs there are three methods for making a final tree Method 1 Save the tree as Nexus format from whatever phylogenetic program you are using Method 2 Save the tree as PHYLIP format Load the tree into PAUP then export the tree use format NEXUS option Method 3 Make a text tree file by yourself as the following
5. Zhang W H Ricklefs R E Qian H Chen Z D Wen J Li J H 2004 Regional differences in rates of plant speciation and molecular evolution a comparison between eastern Asia and eastern North America Evolution 58 2175 2184 Xiang Q Y Manchester S R Thomas D T Zhang W H Fan C 2005 Phylogeny biogeography and molecular dating of cornelian cherries Cornus Cornaceae tracking Tertiary plant migration Evolution 58 1685 1700 Xiang Q Y Thomas D T Zhang W H Manchester S R Murrell Z 2006 Species level phylogeny of the genus Cornus Cornaceae based on molecular and mor phological evidence implications for taxonomy and Tertiary intercontinental migration Taxon 55 9 30 16
6. a fixed tree topology assumed to be without error Nylander et al 2008 A second source of uncertainty in DIVA is that associated with ancestral area optimization multiple equally optimal reconstructions often result in multiple ranges suggested at ancestral nodes Ronquist 1997 Nylander et al 2008 To account for these uncertainties Nylander et al 2008 and Antonellia A et al 2009 recently showed the utility of a non parametric empirical Bayesian approach to DIVA Their approach handles phylogenetic uncertainty and uncertainty in DIVA optimization Harris amp Xiang 2009 proposed an alternative approach to Bayes DIVA which differs in its ability to handle uncertainty at some nodes We have written Statistical Dispersal Vicariance Analysis S DIVA a program which complements DIVA implements the methods of Nylander et al 2008 and Harris and Xiang 2009 and determines statistical support for ancestral range reconstructions using a novel method the S DIVA value In S DIVA the frequencies of an ancestral range at a node in ancestral reconstructions are averaged over all trees and each alternative ancestral range at a node is weighted by the frequency of the node occurring or by some other measure of support for the node S DIVA is easy to install provides a user friendly graphical interface and generates exportable graphical results 1 2 Citation Program Yu Y AJ Harris X He S DIVA Statistical Dispersal Vicariance Analys
7. format tree 6 2 4 9 8 3 1 7 11 10 5 Important Trees with polytomies are not accepted by S DIVA 10 4 2 4 The bare essentials of the final tree Back to Top Final tree files may contain various types of commands and information relevant to the program that created them e g NEXUS Begin trees etc An S DIVA final tree must contain a line of text that looks like tree 6 2 4 9 8 3 1 7 11 10 5 Taxon names must be replaced with integers as shown The unique integer representing each taxon should be the same as in the trees file Other types of information in the final tree file may not hinder S DIVA but are not required Tip What should you do if your consensus tree contains polytomies 1 You can try creating a majority rule consensus tree with compatible groups with less than 50 support allowed 2 Do not use a final tree Instead you can estimate each node individually using Estimate a node 4 3 How to make Distributions file 4 3 1 How to make a Distributions file Back to Top Name the distributions A B C etc and specify multiple area distributions like BD or ACE Only letters from A to O can be used Ronquist 1997 2001 Launch S DIVA Select File gt Load Trees and navigate to your trees data set Select File gt Save Distribution and save it as a csv file Open the your saved csv file in a text editor or Excel Input the distributions after the specie
8. obtain trees data set from BEAST Back to Top Launch BEAUti v exe Select File gt Import Alignment and navigate to your NEXUS input file From our sample files we would select sample 1 nex in the Sample folder Note If BEAUti can t load the NEXUS file then load the file into PAUP and export it use format NEXUS option Select MCMC panel set the number of generations the MCMC algorithm will run for We set length of chain 000000 to do a quick run Click Generate BEAST file and save your file We saved it as samlpe1 xml in sample folder Launch BEAST v exe Enter a Random number seed like 12345 Choose your BEAST XML input file From our sample files we would select sample 1 nex in the Sample folder Run it After the program is finished you will find a trees file in the same folder of your xml file In our example Sample trees is our trees data set 4 1 2 How to obtain trees data set from PAUP Back to Top Use Lset or Pset command set for ML or MP analysis with option Collapse NO Define outgroups and root the trees with roottrees OUTROOT MONOPHYL Save all of your trees using format NEXUS option Important Trees with polytomies are not accepted by S DIVA 4 1 3 How to obtain trees data set from other phylogenetic programs Back to Top If you are using Mrbayes it is helpful to define outgroups and specify rooting before you run memc If you did not define outgro
9. soft and hard polytomies Check your trees for polytomies You may also see this error message if your trees have not been rooted Cannot format the tree The S DIVA program accepts phylogenetic trees a trees dataset and a final tree generated by the programs BEAST Drummond and Rambaut 2006 PAUP Swofford 2003 and MrBayes Huelsenbeck amp Ronquist 2003 Other tree file formats may cause this error The error may also occur if you are using an accepted format but have syntax errors in your file e g a misplaced semicolon a missing end command etc Opening the file using PAUP may help you determine if there is a syntax error and if so what it is Cannot process the computed file There is something wrong with the temp file Please delete the folder Temp and restart the S DIVA Cannot process the trees There is something wrong with the temp file Please restart S DIVA Distributions must be labeled using the letters A to O only Remember that distributions must be labeled using the letters A to O only and should include no more than 15 unit areas S DIVA does not highlight rows containing unrecognized characters Distributions of omitted taxon should not be null When with omitted taxa distributed in is checked you must define the distribution of the omitted taxon Distributions should not be null You have not provided distribution information for one or more taxa S DIVA should highlight rows missing distrib
10. A Rough Guide to S DIVA Yan Yu AJ Harris and Xingjin He March 2 2010 College of Life Sciences Sichuan University Chengdu 610064 China Email yuyan mnh scu edu cn Curriculum for the Environment and Ecology University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 USA Contents A Roush Guide to S DIVA ae e e E e EAE dese cusucudusucu cedaci cucuduseds ceded EE EA EEE E ET EE E E TEER 1 Lalntroduction Back contenti oense a a a AEE E E O O O 3 DD EX OAM atl ON N e E EE EERE LETS 3 Past Ns 3 2 Installiig back tO CONTEATS a T T T T ERE RRS 4 3 Asimple S DIVA tour step by step back to CONTENTS sisvssivsrisssisss isss isisi sssi vason a NEN eno N a NENEN ENEN E NENEN NENEN EVENE E NENNEN NENNEN 5 Jk PLepdldtlon atte ee ea aa ae ee 5 B22 load IN PUE FILES lt ccccccesdeess cccecunsscdueseccceceuneaeouesecoadsaunessoussnesaieeuesauousseesatunue va EEE E E 5 SPAN AVSIS tea ane ean Ree eee a E E N 6 ZA RESUS sneer eae see ae eae So E SIAN PE PU ANP OUTRUN EU EN OEE EE A 7 A HOW 10 BDACKtO CONTENES a E E E 9 4 1 How to make Trees data set ssssssssesrsssssssssserrssssssreesrsssssstreeernsssssstreesrsssssstteerasssssstteeessssssseteeesassssssteeeressssaet 9 4 2 How to make a Final tree esssssssssssesrssssssssreesrsssssssteerrsssssstereersssssstteeesasssssstreerssssssetreesnasssssteeernssssssreeeresssseet 10 4 3 How to make Distributions file sssesssssssssssssssrrsssssssesrrsss
11. Export the trees data set savetrees file C data_set trees replace with your file name format NEXUS root Yes BRLENS Yes SAVEBOOTP BOTH REPLACE YES MAXDECIMALS 0 FROM 1 TO 200001 replace with the total number of your trees Export the final tree CONTREE All PERCENT 50 STRICT No SEMISTRICT No MAJRULE Yes LE50 Yes GRPFREQ Yes ADAM S No INDICES No SHOWTREE Yes treefile c final_tree tre replace with your file name replace yes 6 Launch S DIVA Import your trees data set 7 Rebuild your distributions file The distributions of outgroups should also be defined 8 Import the final tree into S DIVA and run analysis 12 5 10 11 12 13 14 Explanation of messages back to contents Allowing reconstructions will need a larger amount of free space on disk and will take a longer time to run Are you sure to use it User will get this message when the number of taxa is more than 64 and reconstructions are allowedsuch that F x Allow reconstruction will need a larg amount of free space on disk and may take a long time to run n t D t For example processing 100 trees with 84 taxon max areas of each node 4 needs about 5G free space on disk and will take about 2 hours You may click yes to enable Allow reconstructions or click No to disable it Cannot accept polytomies The current version of S DIVA can handle only fully bifurcating trees Future releases of S DIVA may be able to handle
12. he thrushes Aves Turdus Systematic Biology 57 257 268 Ronquist F 1997 Dispersal vicariance analysis A new approach to the quantification of historical biogeography Systematic Biology 46 195 203 Ronquist F 2001 DIVA version 1 2 Computer program for MacOS and Win32 Evolutionary Biology Centre Uppsala University Available at http www ebc uu se systzoo research diva diva html Sanmartin I Enghoff H Ronquist F 2001 Patterns of animal dispersal vicariance and diversification in the Holarctic Biological Journal of the Linnean Society 73 345 390 15 Sanmart n I Ronquist F 2004 Southern Hemisphere biogeography inferred by event based models plant versus animal patterns Systematic Biology 53 216 243 Soltis D E Morris A B MacLachlan J S Manos P S Soltis P S 2006 Comparative phylogeography of unglaciated eastern North America Molecular Ecology 15 4261 4293 Swofford D L 2003 PAUP Phylogenetic Analysis Using Parsimony and Other Methods Version 4 Sinauer Associates Sunderland Massachusetts US Wen J 1999 Evolution of the eastern Asian and eastern North American disjunct distributions in flowering plants Annual Review of Ecology and Systematics 30 421 455 Xiang Q Y Soltis D E Soltis P S 1998 The eastern Asian and eastern and western North American disjunction congruent phylogenetic patterns in seven diverse genera Molecular Phylogenetics and Evolution 10 178 190 Xiang Q Y
13. is VERSION Available at http mnh scu edu cn S DIVA Associated Materials Yu Y Harris AJ He XJ 2010 S DIVA Statistical Dispersal Vicariance Analysis a tool for inferring biogeographic histories Molecular Phylogenetics and Evolution doi 10 1016 j ympev 2010 04 011 Ronquist F 2001 DIVA version 1 2 Computer program for MacOS and Win32 Evolutionary Biology Centre Uppsala University Available at http www ebc uu se systzoo research diva diva html User s Guide Yu Y AJ Harris and X He 2010 A rough guide to S DIVA Available online at http mnh scu edu cn S DIVA Accessed DATE 3 2 l nsta i ng back to contents S DIVA was developed for use on Microsoft Windows operating systems Supported Operating Systems Windows NT 2000 2003 2008 XP Vista and Windows 7 Processor 400 MHz Pentium processor or equivalent Minimum 1GHz Pentium processor or equivalent Recommended RAM 64 MB Minimum 128 MB Recommended Display 800 x 600 256 colors Minimum 1024 x 768 high color 32 bit Recommended For computation of large datasets you should have a fast processor and large amount of free space on disk Note You can use File gt Clean Cache in S DIVA to free the disk space after the analysis S DIVA is distributed without charge by download from the S DIVA web site http mnh scu edu cn S DIVA If someone has given you a copy of S DIVA we strongly suggest that you download the most recent version f
14. length Set the length of branches 10 1000px All branches in the cladogram become proportionately larger or smaller node 19 anc of terminals 5 9 node 20 anc of terminals 10 9 node 21 anc of terminals 10 11 optimal reconstruction number 1 S DIVA Value 677 8640 node 12 anc of terminals 2 1 node 13 anc of terminals 2 3 node 14 anc of terminals 2 4 node 15 anc of terminals 5 4 node 16 anc of terminals 7 6 node 17 anc of terminals 7 8 node 18 anc of terminals 7 9 node 19 anc of terminals 5 9 A node 20 anc of terminals 10 9 node 21 anc of terminals wnd gt hb P P node 18 anc of terminals 7 9 P P f FOOD DED Branch length Taxon separation 50 g Pie radii i Border separation 250 W Distribution Color Pie M Support value Set Zoom fs I Trans bg The node of terminals 2 species_02 to 3 species_03 seems to have originated in area A with 0 99 support value The node of terminals 10 species_10 to 9 species_09 have four possible ancestral ranges A B AB or ABC the occurrence of each range is A 11 B 23 AB 33 ABC 33 The selected node s distributions node 20 terminals 10 9 are displayed as bar chart Taxon separation Set the separation of taxa 10 200 Pie radii Set the radii of pie charts 2 100 Border separation set the width of 10 ABC Species_10 5
15. n undefined sister x I with fossils distributed in m Taxon_10 M Hide status output S DIVA information Window m Optimize Load Sucessfully por ir M Allow Reconstruction een I Max areas at each node Be T Age m Weight 0 5 I wold 1000 M Bound 250 I Set command for final tree Joptimize Printrecs Maxareas 4 Weigh 3 3 Analysis Choose Analysis gt Run Analysis to use default options to run analysis Option Options Amount of trees 100 Amount of trees The total number of trees in your trees data set You can decrease this Burn in 10 number to discard the trees from the end of the trees data set I Random trees 100 Burn in The number of trees that will be discarded from the beginning of the trees data set C Use Tree File Example Amount of trees 10001 and Burn in 1000 means trees from 1001 to 10001 AUR Raa in trees data set will be included in next analysis and all others will be ignored a Use Tree File Run S DIVA analysis for all nodes in the final tree Estimate a node Use DIVA output file Allows you to use an existing DIVA output file as the result of iad the final tree A sample DIVA output file Sample Sample1_DIVA_output txt I With an undefined sister x You may use the following command to get an output file form DIVA I With fossils distributed in echo status IV Hide status output Output OULESE Optimize tree 5 2 1 3 4
16. ontents Alexandre A Johan A A N Claes P Isabel S 2009 Tracing the impact of the Andean uplift on Neotropical plant evolution Proceedings of the National Academy of Sciences of the United States of America 106 24 9749 9754 Donoghue M J Smith S A 2004 Patterns in the assembly of the temperate forest around the Northern Hemisphere Philosophical Transactions of the Royal Society of London Biology 359 1633 1644 Drummond A J and Rambaut A 2006 BEAST v1 4 http beast bio ed ac uk Harris AJ Thomas D T Xiang Q Y 2009 Phylogeny origin and biogeographic history of Aesculus L Sapindales an update from combined analysis of DNA sequences morphology and fossils Taxon 58 108 126 Harris AJ Xiang Q Y 2009 Estimating ancestral distributions of lineages with uncertain sister groups a statistical approach to Dispersal Vicariance Analysis and a case using Aesculus L Sapindaceae including fossils Journal of Systematics and Evolution 47 349 368 Huelsenbeck J P Ronquist F 2003 MrBayes 3 Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 1574 Lamm K S Redelings B D 2009 Reconstructing ancestral ranges in historical biogeography properties and prospects Journal of Systematics and Evolution 47 369 382 Nylander J A A Olsson U Alstr m P Sanmart n I 2008 Accounting for phylogenetic uncertainty in biogeography a Bayesian approach to Dispersal icariance Analysis of t
17. put from BEAST or PAUP A sample final tree sample Sample1_Final_Tree tre How to How to make a final tree using BEAST How to How to make a final tree using PAUP How to How to obtain a final tree from other phylogenetic programs 3 Distributions file not required A sample distributions file sample Sample1_Distribution csv How to How to make a Distributions file How to _How to input distributions in S DIVA 3 2 Load Input Files Launch S DIVA 1 Open File gt Load Trees and navigate to your trees data set and select it Example Open Samplel trees in folder Sample 2 Open File gt Load Computed File gt Load Final Tree and navigate to your final tree file and select it Example Open Sample _Final_Tree tre in folder Sample 3 If you have a distributions file then Open File gt Load Distribution and navigate to your file and select it Example Open Sample Distribution csv in folder Sample You can input and revise the distributions in the entry fields in the Distribution column in S DIVA mso a ioixi File Graphic Analysis PD Taxon Distribution p Option gt 1 Taxon_1 A Amount of trees 100 2 Taxon_2 Cc Burn in 10 3 Taxon_3 A I Random trees 100 4 Taxon_4 D C Use Tree File 5 Taxon_5 c 6 Visual Studio 2008 Projects S DIV 6 Taxon_6 A Use DIVA output file 7 Taxon_7 D 8 Taxon_8 A Estimate a node 9 Taxon_9 B CE D I With a
18. rom this site No installation is needed and you can put the S DIVA exe in any directory you like DIVA 1 2 Ronquist 1997 2001 is bundled in S DIVA You can also download it from here and put it in the directory of S DIVA IMPORTANT If you are using Windows 2000 2003 or XP please make sure that Microsoft NET 2 Framework is installed on your computer This is usually installed through Windows updates but it may be absent from older systems The NET framework 2 packages are available for free here and should be installed prior to using S DIVA For Mac and Linux Users The S DIVA web service http mnh scu edu cn sdiva_web is a good choice for MAC and Linux users We have added a note about the availability of the web service in the Implementation Details Parallels Desktop or VMware Fusion can also be used to run S DIVA on a Mac or Linux The S DIVA web service is still in beta and we recommend the offline version of S DIVA 3 A simple S DIVA tour step by step macto contents 3 1 Preparation You need 1 Trees data set Output from BEAST Drummond and Rambaut 2006 or PAUP Swofford 2003 A sample trees data file sample sample1 tree How to How to obtain trees data set from BEAST How to How to obtain trees data set from PAUP How to How to obtain trees data set from other phylogenetic programs 2 A Final tree not required if you want to estimate a particular node only Out
19. ruction Unchecking this option changes the method used for calculating F x from i D to 1 N See section 3 4 1 below Max areas The number of unit areas allowed in ancestral distributions Weight Age Bound and Hold These four options are the same as in DIVA 1 2 Set command for final tree Set the optimize command for the final tree separately If you need additional help with the Optimize options Max areas Weight Age Bound Hold or with setting the command line we recommend reviewing these options in DIVA 1 2 command help and the DIVA 1 1 User s Manual Ronquist 1996 3 4 Results 3 4 1 Text results If Allow Reconstruction is checked you will see results in the S DIVA information Window that look like this D gt D gt D gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt SSS gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt gt Result optimal distributions at each node node 12 anc of terminals 7 6 B 100 node 13 anc of terminals 7 8 B 100 node 14 anc of terminals 7 9 AB 100 node 15 anc of terminals 2 1 A 100 node 16 anc of terminals 2 3 A 100 node 17 anc of terminals 2 4 A 50 AB 50 node 18 anc of terminals 5 4 B 50 AB 50 node 19 anc of terminals 7 4 A 48 8806 B 51 11941 node 20 anc of terminals 7 10 A 19 31818 B 19 31818 AB 19 31818 ABC 42 04546 node 21 anc of terminals
20. s name like this mal pic 1 1 Species_O1 A 5 Species 05 B 2 2 Species_02 A 6 Species_06 B 3 3 Species_03 A E Species 08 BC 4 4 Species_0 AB 9 Species_09 A or i 5 Species_05 B 4 3 2 How to input distributions in S DIVA Back to Top Name the distributions A B C etc and specify multiple area distributions like BD or ACE Letters from A to O must be used Ronquist 1997 2001 215 x File Graphic Analysis Launch S DIVA D Taxon Distribution pees Select File gt Load Trees and 1 Species_01 A Amount of trees gt 2 Species_02 Bl 101 navigate to your trees data set 3 species 03 Burnin eal 4 10 Type your distributions directly 4 5 Species_05 Use Tree Fle into the Distribution column 6 Species_06 SS 7 Species_07 5 Remember to save the Use DIVA output fie 8 Species_08 distributions you have entered 9 Species09 10 Species_10 J I Random trees 100 to a file for use in future M ante analyses Save the distributions as a csv file using File gt Save Distribution 4 4 Examples 4 4 1 How to process output file from Mrbayes Load your nex file into PAUP Import the trees file generated by Mybayes into PAUP 11 gettrees file c totaldna nex run1 t replace with your trees file Unrooted Yes Define the outgroup outgroup 1 2 3 4 replace with your outgroups ONLY Root the trees roottrees OUTROOT MONOPHYL
21. ssstsreersssssstrecersssssserresrssssssstreeussssssotreesussssseeeeeresssssot 11 MDE E E 11 5 Explanation of messages back to contents cccccesseeseseeseeeeeseeeeeeeeeeeeeeeeeeeeseeeeseesessssssseesseeesseseeesssesseeeaasaaaaaaaaaaea 13 6 References back to contents cccccccessssseesseeeeeeeeeeeee sees esses see A AAAs AAA AAA AA GAGA GAGA AAA A AAA A GAGA AAA A AAA G GAGA GAGA GaGa aaa aaa a aa aaa aaa aaa aa aaaa 15 1 Introduction back to contents 1 1 Explanation Studies in historical biogeography based on phylogeny have accumulated rapidly in the literature due to the exponential increase in phylogenetic studies see Xiang et al 1998 2004 2005 2006 Wen 1999 Sanmart n et al 2001 Donoghue amp Smith 2004 Sanmart n amp Ronquist 2004 Soltis et al 2006 Harris et al 2009 Dispersal Vicariance Analysis DIVA Ronquist 1997 2001 is one of the most widely used methods of inferring biogeographic histories This is evidenced by an advanced Google scholar search for DIVA and biogeography in 2009 returning greater than 50 relevant results DIVA reconstructs the ancestral distribution in a phylogeny by optimizing a three dimensional cost matrix in which extinctions and dispersals cost more than vicariance Ronquist 1997 Lamm amp Redelings 2009 One problem with the current implementation of DIVA is that it ignores the uncertainty in phylogenetic inference because ancestral ranges are reconstructed onto
22. timal reconstruction of the final tree is calculated as sv S PC n l where c is the total number of sampled taxon The total number of node is calculated as c 1 If Allow Reconstruction is not checked you will see results without S DIVA Value anf F x will be calculated as F X 1 N where N is the total number of alternative ancestral distributions at node n Nylander et al 2008 3 4 2 Graphic results After running an analysis a Tree View window will automatically open You can also access this window from Graphic gt Tree View Node list optimal distributions at each node Select a node to display alternative ancestral distributions pie chart and bar chart at the selected node on the tree Select all nodes in the list to display pie charts and distributions for all nodes as in the figure below Bar charts are displayed for only one node at a time optimal reconstruction number lt n gt Select all nodes to display distributions at all nodes from reconstruction lt n gt on the tree Select a single node to display the distribution at that node from reconstruction lt n gt on the tree Display options iok Fie Result node 12 anc of terminals 2 1 P node 13 anc of terminals 2 3 P node 14 anc of terminals 2 4 P node 15 anc of terminals 5 4 P node 16 anc of terminals 7 6 node 17 anc of terminals 7 8 node 12 anc of terminals 2 1 P 0 99 A 100 Branch
23. ups and specify rooting before the MrBayes run you can root all trees using PAUP or other available software You can load the MrBayes output file run t as your trees data set once the trees have been rooted For other phylogenetic programs there are two methods for making a trees data set Method 1 Save the trees as Nexus format from whatever phylogenetic program you are using Method 2 Save the trees as PHYLIP format Load the trees into PAUP then export the trees use format NEXUS option Important Trees with polytomies are not accepted by S DIVA 4 1 4 The bare essentials for the tree file Back to Top Our sample trees file includes considerable amounts of phylogenetic Begin taxa Taxlabels ay program output but here is what a trees file must contain An example Taxon_1 Taxon_2 which can be accepted by S DIVA is shown to the left Leng Your taxa should have unique labels or names upper arrow Taxon_5 Translate your unique taxon names into integers 1 middle Taxon_6 i Taxon_7 arrow These integers are required for the ID field in the S DIVA program hte Your file should contain one or more phylogenetic trees in set Taxon_10 notation lower arrow Many tree generating programs such as PAUP endi MrBAYES etc include a lot of extra information within each tree such as rn branch lengths likelihood values and so on This extra information does not Translate qigy hinder S
24. ution information one at a time If not check your distribution file or the entry fields in the Distribution column in S DIVA to see which cells were left blank You may also prompt this error if your distributions include unrecognized characters DIVA12 is found in processes do you want to end it DIVA1 2 is running on your computer You cannot run DIVA and S DIVA at the same time Burn in error The value of the Burn in must greater than or equal to zero but smaller than the amount the trees error no distribution specified Your group of organisms should include no more than 127 taxa The distributions should include no more than 15 unit areas error no tree specified Your group of organisms should include no more than 127 taxa The distributions should include no more than 15 unit areas error optimal reconstruction requires too many dispersals The optimal reconstruction requires too many dispersals You need to decreases the number of taxa or distributions Missing DIVA results of tree Cannot do the analysis There is something wrong with the temp file Please delete the folder of Temp and restart the S DIVA 13 15 Need at least one tree You need at least one tree in the trees file to run S DIVA 16 Your group of organisms should include no more than 127 taxa Your group of organisms should include no more than 127 taxa The distributions should include no more than 15 unit areas 14 6 References back to c
Download Pdf Manuals
Related Search