Ronquist 1996_DIVA user manual
Contents
1. optimize After some time DIVA should display the results of the optimisation 7 In the result listing each ancestor is identified by a scope of terminals e g ancestor of terminals 1 3 This should be read as the most recent common ancestor of terminals 1 and 3 or the ancestor of terminals 1 2 and 3 The first interpretation is always correct the latter is erroneous if the taxon numbers do not appear in numerical order in the tree description After the definition of the node there will be a list of optimal distributions separated with spaces Areas are identified with http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 13 of 21 letters A being used for the first area B for the second etc Distributions including several unit areas are specified as words such as AB EFG and ACG 8 Further tips If the optimisation is very time consuming or results in a heuristic solution you might want to change some of the default option settings of the optimize command see below If you are interested in identifying a restricted centre of origin for your taxon you can restrict the number of unit areas allowed in ancestral distributions by using the maxareas option of the optimize command Type optimize maxareas x where x is the maximum number of unit areas that you allow Commands by category 1 Utility functions help commands Prints help information about the sp2. segment borders are then prohibited by associating them with infinite cost Like the method developed by descendant state Ronquist and Nylin MC can be formulated as a cost matrix Q k T F optimisation method Because F e as there is a distinction between p zg ae cospeciations and simple tracking z a 7 ge events in MC it is necessary to use http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 5 of 21 a three dimensional step matrix where one axis represents the host of the ancestor and the other two the hosts of the immediate descendants rather than the standard two dimensional matrix Fig 4 The two descendants are equivalent making half the matrix redundant but the matrix is asymmetric in that the ancestor cannot be substituted with any of the descendants This matrix is filled with benefit values specifying whether a cospeciation is possible 1 or impossible 0 given a certain combination of ancestral and descendant hosts By using dynamic programming algorithms similar to those used in optimisation of a two dimensional step matrix it is possible to find the optimal reconstruction of ancestral hosts in the parasite phylogeny Ordinarily one would be interested in finding the mintmum cost reconstruction s In MC however we are trying to find the maximum benefit reconstruction i e the one with the maximum number of cospeciations Event based methods in historical
3. this respect since the success of pattern based methods like that of event based methods is ultimately determined by the relation between the details of the method and the nature of the processes being inferred Event based methods in coevolutionary inference Historical biogeography shares many fundamental concepts and ideas with macroevolutionary comparisons of host and parasite phylogenies Because event based methods were first developed for coevolutionary problems a digression on coevolution may serve as a good introduction to the fundamental issues involved in event based biogeographic reconstruction A common problem in coevolutionary inference may be formulated as follows Given a host phylogeny a parasite phylogeny and an association matrix defining the species or terminal taxa that are currently associated Fig 1 the task is to reconstruct the history of the association or more specifically which ancestral parasites were associated with which hosts To be able to distinguish all branches in the host and parasite trees we will assume that each branch represents a separate species Ronquist and Nylin were the first to A B C propose an event based coevolutionary method to accomplish this task They recognised four types of events in their a hosts model 1 2 3 4 Duplication called broadening of the association by Ronquist and Nylin Exclusion parasites being excluded from or actively avoiding certain hosts Colonisa
4. MV event by event as follows Vicariance Costs nothing in DIVA regardless of the unit areas involved In MV there is a unit benefit if the vicariance event agrees with the general area cladogram otherwise the event is not allowed Duplication Costs nothing in DIVA if it occurs within one area otherwise the cost is equivalent to the number of secondary dispersals needed for two initially allopatric descendants to come to occupy the same set of unit areas that their ancestor did In MV the benefit is zero if the duplication occurs within one unit area or within a combination of unit areas postulated to have formed a contiguous region in the past according to the general area cladogram Otherwise the event is not allowed Extinction Costs one per area deleted in a distribution in DIVA Zero benefit in MV Dispersal Costs one per area added to a distribution in DIVA In MV dispersal is only allowed if it is associated with WN EP Sos i EP speciation A descendant a lineage may then occupy a new EN WP EN WP the general area cladogram The sister species is not allowed to area or a new region of areas disperse it must retain the original distribution until next speciation event The benefit is zero t to postulated to be contiguous in Widespread ancestors Any combination of unit areas allowed in DIVA Only distributions agreeing with the general area cladogram allowed in MV Widespread terminals are problematic in MV they
5. are not used the first distribution is assumed to be that of taxon 1 the second distribution that of taxon 2 etc Examples two equivalent distribution specifications gt distribution test A AB C gt distribution gt 3c gt la gt 2 ab help commands Prints help information about the specified command s If no command is specified the entire help file will be output echo option Determines whether output to file will be echoed to screen Three options are available all Causes all output to be echoed to screen Default setting status Only status reports and error messages are echoed to screen none Nothing is echoed to screen nodeage nodeagespec Sets the ages of the ancestral nodes in a previously specified tree according to the list of values in nodeagespec The order of the ancestral nodes must follow the standard used by DIVA in which nodes are numbered from left to right and from terminals towards the root Fig 10 If you are uncertain about the ordering you can execute an optimize command after a tree and a distribution have been specified and check the numbering of the ancestral nodes in the output If no nodeage command is issued the age of a node is calculated as the maximum number of nodes including the node itself that separates the node from any descendant terminal Example for a six taxon tree with five ancestral nodes nodeage 0 02 0 03 0 10 1 0 2 3 optimize options Reconstruct
6. can be treated either as composite groups with separate lineages each restricted to a single unit area or as cases of uncertainty concerning the original area Compared with MV DIVA has a number of advantages First it is possible to reconstruct the distribution history of individual groups in the absence of a general hypothesis of area relationships Second the model used in DIVA does not assume anything about the shape or existence of general area relationships This means that DIVA reconstructions are likely to fit a hypothesised series of geological events better than MV optimisations particularly if the events do not produce hierarchical area relationships It also makes it possible to use DIVA when different lineages have been affected differently by some series of geological events http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 8 of 21 Dispersal vicariance reconstructions for different groups of organisms inhabiting the same set of unit areas may be assembled and compared to allow testing of hypotheses about general biogeographic events regardless of whether these events produced hierarchically nested area relationships However it is important to consider exactly under what circumstances we might be able to retrieve reticulate area relationships Assume that we have two sister species which occur in area A and B and that we infer correctly that their ancestor occurred in A B
7. has one or more polytomies all possible resolutions may have to be entered separately to allow incorporation of the data in summary statistics To avoid weighting polytomous groups more heavily than others such arbitrary resolutions can be downweighted the weight of each reconstruction is set to 1 0 by default speciation level Ancestral nodes commonly 0 have several equally optimal ancestral distributions qi aen Summary statistics can be calculated only for those nodes http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 10 of 21 with single unambiguous distributions or for all nodes In the latter case the program goes through all possible equally optimal reconstructions Each reconstruction is then weighted such that the sum of all reconstructions is unity Thus an event occurring in all reconstructions will obtain a frequency of 1 0 whereas an event occurring in only one reconstruction of 20 will obtain a frequency of 0 05 Even when the distribution assignments are unequivocal there may be several equally optimal combinations of events producing these distributions as noted above Fig 9 For each of these cases the program goes through all possible combinations of events and weights each combination of events in proportion to the number of possibilities Thus if there are two possible events Fig 9 each event is assigned the frequency 0 5 The age of vicar
8. in ancestral distributions using the maxareas option of the optimize command in DIVA Using this approach we are asking the question If this group had a restricted distribution in the past maximally n unit areas what is the most likely ancestral distribution of the group Terminals are higher taxa If the terminals in an analysis are higher taxa such as genera or families it is important to recognise that one cannot simply add the distributions of the species belonging to the higher taxon A higher taxon should be coded for the likely ancestral distribution not as being distributed in all areas where descendants occur The problem is exactly the same as that which appears with polymorphic higher taxa in the optimisation of morphological characters If the taxon is coded for all states occurring in the taxon information important for the optimisation of ancestral states will be lost There are three approaches one could use to deal with widespread higher taxa First one might try to http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 9 of 21 resolve lower level relationships within the taxon and use these to reconstruct the likely ancestral distribution Second one might infer likely ancestral distributions using the common equals primitive criterion Some caution is needed here but if common is interpreted as common in basal lineages the criterion is clearly applicable Third it
9. is possible to code the higher taxon as being distributed in all areas where descendants occur and use the maxareas option in DIVA to restrict the number of unit areas that may have been occupied by any ancestral species ABC CDE ABC cpe Ambiguous events Frequently there are several alternative distributions at an ancestral node However even when there is a single C C unambiguous state for each node in the tree ABCDE AB CDE there may be several equally costly combinations of events that can explain these distributions Consider a pattern for which the single optimal reconstruction implies that the descendant distributions resulted from vicariance followed by secondary dispersal across the primary dispersal barrier Fig 9 The vicariance might have involved separation of AB from CDE with secondary dispersal of the left descendant into C Fig 9a or separation of ABC from DE with secondary dispersal of the right descendant into C Fig 9b Both alternatives include one vicariance event and one dispersal event Polytomies The current version of DIVA can only handle fully bifurcate trees To infer ancestral areas in polytomous cladograms under the assumption that the polytomies represent uncertainty soft polytomies it is necessary to enter all possible fully bifurcate trees separately and then summarise the results If the polytomous tree is a consensus tree it would be more appropriate to run DIVA separately on each of the trees fro
10. then return control to the console window output filename Redirects output to the specified file The file will be created in the same folder as DIVA DIVA can only create new files it cannot overwrite or append to existing files The setting of echo determines whether the output will be echoed to screen If filename is the output file is closed and output is redirected to the screen console http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 14 of 21 quit Terminates the program The program may also be terminated by clicking the close box choosing quit from the File menu Mac or typing command Q Mac or control C Win In the Macintosh version you will be asked whether or not you want to save the contents of the console buffer before you close You can also print the contents of the console buffer in the Macintosh version When DIVA is processing a command you can stop it by typing command period Mac or b Windows 2 Basic functions tree treename treespec This command sets a tree structure Treename is an optional label maximally 16 characters long Treespec is a tree specification in NEXUS parenthetical format The tree has to be fully bifurcate and contain no more than 180 taxa Taxa may be labelled using any combination of printing characters except comma and parentheses but a consecutive series of integers between and the number of taxa is recomme
11. A simple DIVA run step by step I assume that you have a fully bifurcate phylogeny of your favourite group of organisms no more than 180 taxa and data on their distributions in terms of 15 or less unit areas and would like to reconstruct the ancestral distributions using DIVA This is how to run a simple DIVA analysis on the MacIntosh 1 Use MacClade to create a NEXUS file with a character matrix entirely restricted to binary distribution characters each character recording whether a species terminal taxon is present 1 or absent 0 in a particular unit area cf Fig 4 2 In the tree window construct or import the tree you are interested in so that MacClade stores it in the NEXUS file Save the file If there is only one tree in the file go to step 4 else continue with 3 3 Open the NEXUS file in your favourite word processor Delete all trees except the one that you are interested in Alternatively move the tree description so that it will be last DIVA will ignore all tree descriptions except the last Save the NEXUS file in text only format 4 Move the NEXUS file to the DIVA folder Record the exact name of the file 5 Launch DIVA and run the NEXUS file by typing proc name where name is the name of the NEXUS file DIVA should display the following lines distribution matrix read successfully tree untitled or whatever your tree is called read successfully end of file control returned to console 6 Type
12. DIVA 1 1 User s Manual Page 1 of 21 Swedish English Uppsala University Home Research Information Staff Department of Systematic Zoology UPPSALA UNIVERSITY DIVA 1 1 User s Manual 5 November 1996 Fredrik Ronquist Dep Systematic Zoology Evolutionary Biology Centre Uppsala University Norbyvagen 18 D SE 752 36 Uppsala Sweden email fredrik ronquist ebc uu se Introduction DIVA is a simple program for reconstructing ancestral distributions in a phylogeny using dispersal vicariance analysis DIVA a method in which ancestral distributions are inferred based on a three dimensional cost matrix derived from a simple biogeographic model Unlike other methods in historical biogeography DIVA does not assume anything about the shape or existence of general biogeographic patterns Therefore DIVA is particularly useful in reconstructing the distribution history of a group of organisms in the absence of a general hypothesis of area relationships taxon biogeography The method remains applicable even when area relationships are expected to be reticulate rather than hierarchic Dispersal vicariance reconstructions obtained for different groups of organisms inhabiting the same areas may be collated and used to infer general biogeographic patterns area biogeography For this purpose the DIVA program provides several ways of summarising information in sets of taxon based reconstructions Citation availabi
13. Fig 8 According to the reticulate biogeographic scenario to the left in Fig 8 we would expect this ancestor to stem either from A or B before the union of the areas The only chance to determine this centre of origin correctly would be if some related species stemming from the same centre of origin remained unaffected by the union of A with B Thus reticulate area relationships can only be detected if some species fail to expand their distributions despite the disappearance of dispersal barriers DIVA attempts to find such archaic remnants and if they are found utilises the information in retrieving reticulate area relationships MV on the other hand assumes that narrowly distributed old lineages are the result of extinction of more widely distributed ancestors A possible disadvantage with the DIVA approach is that extinction is not modelled realistically Actually extinction events will never appear in dispersal vicariance optimisations unless geographic constraints are used to modify the original cost assignment rules MV on the other hand may make too frequent use of extinction events in explaining away misfits to a hierarchic general area cladogram Think of three dimensional cost matrices as the generic approach in historical biogeographic and coevolutionary inference DIVA and MV represent simple methods falling within this framework just like Fitch and Wagner parsimony represent special cases of character reconstruction based on co
14. IVA since the program can only store one tree at a time quit Terminates the program The program may also be terminated by clicking the close box choosing quit from the File menu Mac or typing command Q Mac or control C Win In the Macintosh version you will be asked whether or not you want to save the contents of the console buffer before you close You can also print the contents of the console buffer in the Macintosh version When DIVA is processing a command you can http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 19 of 21 stop it by typing command period Mac or b Windows rarefy filename output filename2 areas distributionspec options This command is used to examine the effects of random extinction in certain areas First the frequency of occurrence in the areas in distributionspec is calculated for the optimize commands in the specified batch file filename1 Second occurrences in the areas in distributionspec are randomly deleted such that the frequencies in the areas become equal The result is written to a new batch file filename2 Options nrep x Sets the number of replications to x Default setting is 1 seed x Feeds the pseudorandom number generator the seed x The default is 1 reset options Resets the counters for summary statistics Six options are available ambiguous unambiguous Determines whether or not ancestral nodes for
15. anual html 30 03 2009 DIVA 1 1 User s Manual Page 2 of 21 will assume in this manual that all batch files and NEXUS files that DIVA works with are in the same folder directory as the program Bugs in pre release versions Pre release versions of DIVA versions 0 9 1 0 1 0a and 1 0b contain a bug that with a low probability causes the program to include spurious distributions in the optimal reconstructions Results based on these versions of DIVA should therefore not be published Background Analytical protocols in historical biogeography and coevolution may be divided into event based methods and pattern based methods Brooks parsimony analysis ancestral area analysis and component analysis are examples of pattern based methods These methods measure the fit of data to a particular coevolutionary or biogeographic scenario in abstract units like items of error reversals or homoplasy Therefore pattern based methods are prone to give results that imply contradictory or highly improbable underlying mechanisms such as derived species evolving into their ancestors or irreversible dispersal away from an ancestral area By explicitly basing biogeographic and coevolutionary inference on models of the events involved such contradictions can be avoided Event based methods have been criticised because the accuracy of the result depends on the validity of the model However there is no fundamental difference between the approaches in
16. are set assuming that apple is taxon 1 pear is taxon 2 l is taxon 3 etc References Bremer K 1992 Ancestral areas A cladistic reinterpretation of the center of origin concept Syst Biol 41 436 445 Bremer K 1995 Ancestral areas Optimization and probability Syst Biol 44 255 259 Brooks D R 1990 Parsimony analysis in historical biogeography and coevolution Methodological and theoretical update Syst Zool 39 14 30 Enghoff H 1996 Historical biogeography of the Holarctic Area relationships ancestral areas and dispersal of non marine animals Cladistics 11 223 263 Lynch J D 1989 The gauge of speciation On the frequencies of modes of speciation In Speciation and its consequences edited by D Otte and J A Endler Sinauer Sunderland Nelson G and N I Platnick 1981 Systematics and biogeography Cladistics and vicariance Columbia University Press New York Page R D M 1990 Component analysis A valiant failure Cladistics 6 119 136 Page R D M 1995 Parallel phylogenies Reconstructing the history of host parasite assemblages Cladistics 10 155 173 Ronquist F 1994 Ancestral areas and parsimony Syst Biol 43 267 274 Ronquist F 1996 Reconstructing the history of host parasite associations using generalised parsimony Cladistics 11 73 89 Ronquist F 1997 Dispersal vicariance analysis A new approach to the quantification of historical biogeography Syst Biol 46 000 000 Ronquis
17. atch file to return control to the screen console window Any contents of the batch file after the return command will be ignored by DIVA If there is no return command at the end of the batch file DIVA will read the file to the end and then return control to the console window http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 20 of 21 sum option Prints summary statistics for the optimizations performed since the last reset statement or since the start of the program One option areas x Constrains the output to the first x areas x must be smaller than or equal to the number of areas summed The default value is the number of areas summed or the number of areas encountered in the terminals depending on which is smaller tree treename treespec This command sets a tree structure Treename is an optional label maximally 16 characters long Treespec is a tree specification in NEXUS parenthetical format The tree has to be fully bifurcate and contain no more than 180 taxa Taxa may be labelled using any combination of printing characters except comma and parentheses but a consecutive series of integers between and the number of taxa is recommended Examples gt tree example 1 2 3 4 5 gt tree 1 2 3 4 5 gt tree gt tree apple pear 1 orange banana If the labels in the last example do not correspond to previously used taxon labels new labels
18. biogeography Much of the theory of coevolutionary inference can be translated directly to historical biogeography by substituting area for host Take the problem formulation in coevolution Fig 1 The host phylogeny corresponds to a general area cladogram the parasite phylogeny to a phylogeny of a group of organisms inhabiting those areas and the association matrix to a distribution matrix specifying for each area whether a species occurs in the area 1 or is absent 0 Fig 5 The task in historical biogeography is often to formulate a general area cladogram from a set of organism phylogenies and the associated distribution matrices area biogeography However we may also be interested in reconstructing the ancestral distributions of a particular group of organisms taxon biogeography If in the latter case we have access to a general area cladogram the problem corresponds exactly to that in coevolutionary inference discussed previously A B C Maximum vicariance Let us examine MC as it would apply to problems in historical biogeography The events translate easily cospeciations correspond to vicariance events duplications to sympatric speciation host switches to dispersal and sorting events to extinction Table 1 Since c cospeciations are substituted with organisms vicariance events it would seem b appropriate to refer to the method as the maximum vicariance method MV The assumption that there is a host phylogeny
19. c organisms should reflect the reticulate geologic history Application of MV to Holarctic organisms is likely to yield reconstructions with little explanatory power Dispersal vicariance analysis Dispersal vicariance analysis DIVA represents a new event based approach to biogeographic inference It reconstructs ancestral distributions based on a simple biogeographic model that does not take general area relationships into account Thus it is possible to use DIVA in taxon biogeography even when no general area cladogram is available http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 7 of 21 The premises are as follows Assume that the distributions of extant species and their ancestors can be described in terms of a set of unit areas The optimal reconstruction of ancestral distributions is obtained by optimisation of a three dimensional cost matrix derived using the following simple rules 1 Speciation is assumed to be by vicariance separating a wide distribution into two mutually exclusive sets of areas This event costs nothing 2 A species occurring in a single area may speciate within the area by allopatric or possibly sympatric speciation giving rise to two descendants occurring in the same area The cost is zero 3 Dispersal costs one per unit area added to a distribution 4 Extinction costs one per unit area deleted from a distribution It is possible to compare DIVA and
20. dichotomous trees particularly if there are many terminals Fourth and perhaps most importantly it is necessary to assume that area relationships are hierarchical Being organisms hosts are expected to show hierarchical ancestor descendant relationships Areas on the other hand are not subject to hierarchical cladogenesis Areas change configurations with time as terranes are created fragmented dislocated distorted and destroyed Through these events dispersal barriers that affect many groups of organisms simultaneously appear and disappear Yet we cannot expect these processes to produce hierarchical area relationships more often than they produce reticulate relationships Branching area relationships appear only as the result of the successive appearance of dispersal barriers dividing a once contiguous region in ever smaller isolated areas Common geological events such as establishment of contact between previously separated land masses and retrogression of midcontinental seaways create opportunities for nonrandom dispersal of terrestrial organisms producing reticulate area relationships Similar events affect marine organisms For a simple example consider the geologic history of the major Holarctic regions in the Cenozoic Fig 7 simplified The current continents were formed from separate western and eastern areas which were previously joined into palaeocontinents combining the areas differently The distribution history of Holarcti
21. ecified command s If no command is specified the entire helpfile will be output echo option Determines whether output to file will be echoed to screen Three options are available all Causes all output to be echoed to screen Default setting status Only status reports and error messages are echoed to screen none Nothing is echoed to screen proc filename Changes control from screen to the batch file named filename The batch file must specify a series of commands as they would have been typed in from the keyboard It must be a text file and it must be in the same folder as DIVA unless a correct file path is specified Control is returned to the screen console when proc or return is encountered or when the end of the file is reached A batch file cannot be created in DIVA Instead you will have to use a word processing program and save the file in text only format The proc command can also be used to process NEXUS files containing a presence absence distribution matrix and a tree specification If the NEXUS file contains several tree descriptions only the last will be retained by DIVA since the program can only store one tree at a time return Used at the end of a batch file to return control to the screen console window Any contents of the batch file after the return command will be ignored by DIVA If there is no return command at the end of the batch file DIVA will read the file to the end and
22. eneral In active association systems changes in the association matrix would necessarily be tied to changes in parasite and host traits regardless of whether or not the a b cause of these changes were cospeciation Thus tracking events would be of primary importance in such systems not cospeciation events With this perspective spatially separated parasites and hosts really represent question marks in the association matrix we do not know whether they would be associated had they been in contact In MC analyses on the other hand it must be acknowledged that the cause of cospeciation may be biogeographic common dispersal barriers rather than coevolutionary changes in host and parasite traits particularly in the analysis of passive association systems Finally the algorithms presented by Page may produce spurious results in some cases The reason is that some combinations of host switches that are contradictory are not prohibited in Page s algorithms not even in the exact algorithm The problematic combinations include switches from an original host via an intermediate host to hosts that had gone extinct before the appearance of the original host Fig 3a This problem is currently being addressed Page pers comm The same type of problem occurs in mapping of a host step matrix onto a parasite phylogeny In this context it can be solved by dividing branches into time segments Fig 3b Switches backwards in time across
23. eration system specific routines and was compiled with Metrowerks Code Warrior The source code is included in http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 11 of 21 the program package for the benefit of those interested in modifying the program or examining the particular programming techniques that I used I am not an expert C programmer I learned C while developing DIVA The program evolved considerably from its conception including the addition of many new features along the way and a change of compiler just before the program was completed This means that the code is far from as efficient and elegant as it could have been DIVA was developed for my own research needs I have not had the time to do extensive beta testing particularly not of the features that were added recently Therefore make sure that you save all documents before launching DIVA and save search results often for instance by printing them to an output file with the output command Search techniques used in DIVA The fundamental algorithms used in DIVA are described by Ronquist Rather than calculating the three dimensional cost matrix before the optimisation the cost values are calculated as needed Very little time is lost because the equations are simple and one saves an enormous amount of computer memory that would otherwise have been occupied by the cost matrix a full cost matrix for 15 unit area
24. ets an upper bound x to the length of the optimal reconstruction This will in most cases speed up the optimization and increase the chances of finding an exact solution The value of x must be smaller than 250 which is the default value http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 15 of 21 maxareas x Constrains ancestral distributions to contain maximally x unit areas The value of x must be in the range 2 to 15 The default value is the total number of unit areas inhabited by the terminals The speed of the optimization is strongly dependent on the value of maxareas The smaller the value the faster the optimisation hold x Sets the maximum number of alternative reconstructions that will be kept at a node The value of x must be smaller than or equal to 32 767 The default value is 1000 If hold is set to 32 767 the optimisation is guaranteed to be exact keep x Equivalent to hold x age x Sets the age of the deepest node in the tree This value is used in the calculation of summary statistics if relative age classes are chosen The default value is 1 0 weight x Sets the weight for a particular optimization to x which must be between 0 and 1 The weight is used in the calculation of summary statistics The default value is 1 0 printrecs Prints all alternative equally optimal reconstructions If printrecs is not requested output is restricted to a summary of the opt
25. h or These lines are ignored but they are echoed to screen if present in a batch file Invisible comments can be put inside square brackets Comments within square brackets are removed before lines are being processed This means that they can be inserted e g between commands and their arguments Commands that take a long time to execute notably the optimize command can be interrupted at any time by pressing command period in the Macintosh version of DIVA or b in the Windows version When entering commands it is necessary to enter the full name of the command and finish with a semicolon If it is not possible to fit a command with its arguments and options in a single line just finish the line with carriage return and continue typing on the next line Alternatively just continue typing DIVA will not process the command until semicolon is encountered in a line fed to the program by hitting return Case is ignored in all input Please note that Macintosh and Windows systems have different text file formats Thus you cannot copy a NEXUS file on a MacIntosh computer onto a PC disk and then run the file successfully on a Windows machine Instead either 1 open the NEXUS file in a word processor on the MacIntosh and save it in MS DOS text format before copying it onto the PC disk or 2 open the file in a word processor on the Windows machine and save it in text format before using it as a batch file in DIVA
26. i e a hierarchical set of host relationships translates to an assumption that there is a general hierarchical set of area relationships a general area cladogram The one host per parasite assumption corresponds to a one area per species assumption This means that ancestral species are allowed to occur in single areas or in multiple areas postulated to have formed a contiguous region in the past according to the general area cladogram Ancestral species are not allowed to occur simultaneously in areas that could not have been contiguous according to the area cladogram nor are they allowed to be restricted to a smaller part of a contiguous region area a cladogram Mo w A species MV has several limitations some of which are C luti Bi h EE A PERENE I inherited from MC and some of which relate to Cospeciation Vicariance allopatric special challenges posed by problems in historical speciation biogeography First MV suffers from several a ae i constraining assumptions e g that dispersal is Duplication Duplication sympatric associated with speciation see discussion above speciation for MC and that widespread ancestors are not http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 6 of 21 allowed the one area per species assumption Host switch Di 1 with iated ee PEE ors Second it is impossible to do taxon biogeography extinction with MV unles
27. iance events and distributions correspond directly to the age of the ancestral node to which they belong Dispersal events however occur along internodes and may therefore be assigned any date from the age of the ancestral node incident to the branch to the age of the descendant node incident to the branch DIVA arbitrarily uses the age of the ancestral node DIVA only deals with dispersals in which both the ancestral and the target areas can be identified unambiguously Thus the dispersals considered in the summary statistics only include those where an ancestor occurring in a single area colonises a second area When using DIVA in area biogeography the possible existence of reticulate area relationships must be acknowledged Thus it is inappropriate to use the term general area cladogram and I suggest using the term biogeographic scenario instead Such scenarios take the form of a number of time segments in each of which some unit areas are postulated to be connected and others to be isolated cf Figs 6 7 Between time segments contiguous multi area units split by the appearance of dispersal barriers and isolated areas come into contact ideally segment borders are chosen such that these events occur between and not within time segments How can summary statistics from DIVA be used to reconstruct or test such biogeographic scenarios Within a time segment simply study the frequency of different distributions Multi area distributi
28. imal most parsimonious distributions at each node 3 Functions for summary information nodeage nodeagespec Sets the ages of the ancestral nodes in a previously specified tree according to the list of values in nodeagespec The order of the ancestral nodes must follow the standard used by DIVA in which nodes are numbered from left to right and from terminals towards the root Fig 11 If you are uncertain about the ordering you can execute an optimize command after a tree and a distribution have been specified and check the numbering of the ancestral nodes in the output If no nodeage command is issued the age of a node is calculated as the maximum number of nodes including the node itself that separates the node from any descendant terminal Example for a six taxon tree with five ancestral nodes nodeage 0 02 0 03 0 10 1 0 2 3 reset options Resets the counters for summary iz 14 15 i7 statistics Six options are available ambiguous unambiguous Determines whether or not ancestral nodes for which the optimal 20 distribution is ambiguous will be included in summary statistics Default setting is to include ambiguous ancestral distributions http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 16 of 21 relative absolute Determines the type of time classes used Absolute time classes are defined by the number of speciations separating ancestral nodes from terminal
29. lity and disclaimer Cite this manual and the DIVA program as Ronquist F 1996 DIVA version 1 1 Computer program and manual available by anonymous FTP from Uppsala University ftp uu se or ftp systbot uu se The program and manual may be copied and distributed freely provided that the source of results or ideas is cited The source code is available from the same FTP sites and may be copied modified and recompiled as desired There are no warranties neither express nor implied The program may contain bugs that will crash your system or overwrite sectors of your hard disk Be sure to keep backups of all important documents and software and save all your work before launching DIVA Installation There are three versions of the program 1 DIVAppc runs natively on Power Macs 2 DIVA68K runs on the old Macintoshes system 7 0 and later and in emulated slower mode on Power Macs 3 DIVA exe is for 32 bit Windows systems including Windows 3 x with Win32S installed Windows95 and Windows NT The different versions of DIVA behave almost identically and will only be distinguished herein when necessary DIVA requests 1 MB of memory but it will run successfully with much less However the amount of available memory may limit the possibilities of obtaining exact solutions for complicated problems To install the program simply copy it to the desired folder directory For simplicity I http www ebc uu se systzoo research diva manual dm
30. m which the consensus was calculated In some cases it may be possible to combine taxa in polytomies with the same distribution into a single taxon to reduce the number of arbitrary resolutions Future releases of DIVA may be able to handle soft and hard polytomies Dispersal vicariance analysis and area biogeography DIVA provides several features for summarising information in sets of reconstructions The most basic functions simply summarise the frequency of events such as particular vicariance or dispersal events The more advanced functions sort the events into time classes based on estimated dates for the ancestral nodes If there is some source of branch length estimates the node ages can be entered manually using the nodeage command DIVA can also calculate rough node ages using a simple speciation level measure which is based on the maximum number of nodes separating a particular node from any subtended terminal including the node itself Fig 10 This corresponds to the maximum number of speciations as evidenced by the cladogram separating the ancestor corresponding to the node from any terminal Several additional features in DIVA facilitate compilation of information in sets of reconstructions If the ages of the ancestral nodes in two cladograms are not comparable it is possible to provide the age of the root node in each group by default set to 1 0 to calibrate the ages of the ancestral nodes If one of the source cladograms
31. nded Examples gt tree example 1 2 3 4 5 gt tree 1 2 3 4 5 gt tree apple pear 1 orange banana If the labels in the last example do not correspond to previously used taxon labels new labels are set assuming that apple is taxon 1 pear is taxon 2 l is taxon 3 etc distribution distributionname distributionspec This command sets the distributions of a set of terminal taxa Distributionname is an optional label maximally 16 characters long The label must begin with otherwise it will be interpreted as a distribution Distributionspec is a list of the distributions of the terminal taxa in terms of unit areas maximally 15 Name the distributions A B C etc and specify multiple area distributions like BD or ACE Letters from A to O must be used The distributions may be preceded by numeric labels corresponding to taxon numbers If such labels are not used the first distribution is assumed to be that of taxon 1 the second distribution that of taxon 2 etc Examples two equivalent distribution specifications gt distribution test A AB C gt distribution gt 3c gt la gt 2 ab optimize options Reconstructs the optimal distribution s of the ancestral nodes in the last tree specified Depending on the setting of parameters and the difficulty of the problem the optimisation is either exact or heuristic signalled in output The following options are available bound x S
32. ntered in the terminals depending on which is smaller 4 Rarefaction function rarefy filenamel output filename2 areas distributionspec options This command is used to examine the effects of random extinction in certain areas First the frequency of occurrence in the areas in distributionspec is calculated for the optimize commands in the specified batch file filename1 Second occurrences in the areas in distributionspec are randomly deleted such that the frequencies in the areas become equal The result is written to a new batch file filename2 Options nrep x Sets the number of replications to x Default setting is 1 seed x Feeds the pseudorandom number generator the seed x The default is 1 Commands in alphabetical order http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 17 of 21 distribution distributionname distributionspec This command sets the distributions of a set of terminal taxa Distributionname is an optional label maximally 16 characters long The label must begin with otherwise it will be interpreted as a distribution Distributionspec is a list of the distributions of the terminal taxa in terms of unit areas maximally 15 Name the distributions A B C etc and specify multiple area distributions like BD or ACE Letters from A to O must be used The distributions may be preceded by numeric labels corresponding to taxon numbers If such labels
33. nts Page acknowledged the difficulties involved in trying to determine a relative cost for each of the four types of events and suggested as a first simple approach to choose reconstructions that maximise the number of cospeciations He also presented algorithms for optimising this criterion implemented in the program TreeMap available from Rod s home page http taxonomy zoology gla ac uk rod rod html Page s maximum cospeciation method MC provides a powerful analytical tool in coevolutionary inference but there are some important limitations that one should be aware of First it is necessary to assume that host switches are always associated with speciation these speciation events cannot then be cospeciations and that only one of the two resulting daughter species shifts to a new host If these constraints were not imposed it would be possible to assign cospeciation events to all of the ancestral parasite nodes regardless of the host associations of the terminals by simply allowing enough host shifts on the terminal branches Second MC is similar to a clique method in that it only considers one type of events Thus the maximum cospeciation reconstruction will be preferred even though it might be possible to reduce the number of duplications sorting events and host switches considerably by assuming slightly fewer cospeciations A B C B C Third one has to accept the focus on cospeciation events rather than on tracking events in g
34. o compare the mapping results obtained with different relative switch costs and find the optimal switching tracking cost ratio for a particular association A simple example may illustrate the construction of a host step matrix Fig 2 There are only two host species A and B and their ancestor C To move from A or B to C is impossible associated with infinite cost because C is the ancestor of A and B and ceased to exist when A and B were formed To move from A to B or vice versa costs one host switching event cost s To move from C to B or from C to A implies one host tracking event cost t Finally remaining on the same host after speciation represents duplication and costs nothing the diagonal row of zeros Page recently proposed a different event based method to reconstruct the history of host parasite associations under the one host per parasite assumption He recognised four different types of events in his model Duplication Host switching colonisation and exclusion combined http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 4 of 21 e Sorting events host tracking without cospeciation e Cospeciation host tracking through cospeciation The events considered in Page s model correspond closely to those in the cost matrix approach developed by Ronquist and Nylin the only important difference is that Page separates host tracking into cospeciation and sorting eve
35. ons that were common in the time interval demonstrate the connection of unit areas Similarly frequent dispersals between areas indicate that the areas were connected Strong dispersal asymmetries between two areas suggest that the fauna or flora of one area successfully invaded that of the other area Undoubtedly the precision of the estimated ages of the ancestral nodes is the limiting factor in the analyses of biogeographic scenarios with DIVA Most data sets do not have accurate branch length estimates and the speciation level measure used by DIVA is too coarse to allow anything but very superficial analyses However in the future we will undoubtedly see more data sets with estimates of branch lengths or ages of ancestral nodes and more refined methods of inferring these parameters allowing more powerful analyses of biogeographic scenarios The DIVA program General properties of the program DIVA is entirely controlled by commands entered from the keyboard or processed in a batch file This gives the program flexibility while keeping it small and portable It has also saved me from spending valuable time learning how to write full fledged Mac OS and Windows applications However it does mean that the user interface is archaic in appearance and that you will have to consult the manual often in order to be able to run the program correctly I apologise for that DIVA was written in ANSI compliant C code complemented with a few calls to op
36. s Relative time classes are defined by the ratio between the number of speciations for an ancestral node and the number of speciations for the deepest node in the cladogram multiplied by the age of the group The default setting is absolute classes x Defines the number of time classes used The number must be smaller than or equal to 5 The default value is 1 interval x Sets the width of the time classes except the oldest one If absolute is specified the value must be an integer Default setting is 5 for absolute time classes and 0 5 for relative time classes bounds n x1 x2 xn Allows the user to specify time classes of unequal size The number of bounds is specified by an integer n Following this is a list of integer or floating point numbers x etc specifying the upper bound of all classes except the oldest one If bounds are not given for all classes the interval value is used to obtain the missing bound values sumareas x Constrains the summation to only consider the first x areas The value of x must be in the range from 0 to 8 The default value is 0 no information summarized sum option Prints summary statistics for the optimizations performed since the last reset statement or since the start of the program One option areas x Constrains the output to the first x areas x must be smaller than or equal to the number of areas summed The default value is the number of areas summed or the number of areas encou
37. s corresponding to 32 767 different distributions would occupy about 15 000 GB of memory In contrast to standard cost matrix optimisation DIVA attempts to take shortcuts based on the structure of the data A few simple rules are used to limit the number of possible optimal distributions for each ancestor prior to the down pass In most cases these rules will be successful in simplifying the problem considerably However the optimisation may take an enormous amount of time if there are many widespread terminals in which case a large number of alternative ancestral distributions have to be taken into account For such problems the strategy used by DIVA will be inefficient and waste memory On the other hand the results from these analyses will anyway be uninformative in that most nodes will have a large number of alternative distributions By default DIVA will save only the 1 000 most optimal distributions for each ancestral node However one area distributions are always kept even though they are not among the most optimal alternatives because they may gain significantly over multi area distributions in the uppass of the algorithm The number of alternatives to keep at each node can be set from 1 to 32 767 the latter number guarantees that all possible ancestral distributions for 15 unit areas can be kept Going through a large number of possible distributions will take a long time on most computers To speed up the optimisation you might wan
38. s a single host at any single point in time the one host per parasite assumption This would seem a reasonable assumption for intimate associations the systems that would be most likely to be historically constrained Under the one host per parasite assumption only three kinds of events are possible in optimal reconstructions e Duplication null expectation e Host switching colonisation of a new host and exclusion from the old host e Host tracking equivalent to successive specialisation The importance of the one host per parasite assumption is that it allows one to use standard cost matrix optimisation methods which assume that ancestors are monomorphic to map hosts onto the parasite phylogeny Note that it would not be possible to do it the other way round Even under the one host per parasite assumption it is permissible for several parasites to attack the same host and standard techniques could therefore not be used to map parasites onto the host phylogeny If duplications are expected then we need only determine the cost of host switches relative to that of tracking events Assume that this value is given Then a step matrix specifying the cost of moving between different ancestral and or extant hosts can be constructed and standard optimisation of this complex host matrix character onto the parasite phylogeny gives the minimum cost reconstruction of the history of the association By using a suitable fit function it is possible t
39. s the optimal distribution s of the ancestral nodes in the last tree specified Depending on the setting of parameters and the difficulty of the problem the optimisation is either exact or heuristic signalled in output The following options are available bound x Sets an upper bound x to the length of the optimal reconstruction This will in most http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 18 of 21 cases speed up the optimization and increase the chances of finding an exact solution The value of x must be smaller than 250 which is the default value maxareas x Constrains ancestral distributions to contain maximally x unit areas The value of x must be in the range 2 to 15 The default value is the total number of unit areas inhabited by the terminals The speed of the optimization is strongly dependent on the value of maxareas The smaller the value the faster the optimisation hold x Sets the maximum number of alternative reconstructions that will be kept at a node The value of x must be smaller than or equal to 32 767 The default value is 1 000 If hold is set to 32 767 the optimisation is guaranteed to be exact keep x Equivalent to hold x age x Sets the age of the deepest node in the tree This value is used in the calculation of summary statistics if relative age classes are chosen The default value is 1 0 weight x Sets the weight for a particular optimi
40. s there is a general area cladogram Sorting Extinction available Reconstructing ancestral areas using event MV is simply inappropriate in the absence of a general hypothesis of area relationships A B C D Third there is no available automated search strategy for finding the general area cladogram with the maximum number of vicariance events from a set of organism phylogenies and associated distribution matrices However such analyses would certainly be possible and we might expect to see important developments in this field Many of the usual tree search strategies could undoubtedly be adapted for such problems in area biogeography MV character optimisation is considerably more time consuming than ordinary Fitch or Wagner optimisation necessitating the use of heuristic searches even for quite limited problems but techniques such as stepwise addition and branch swapping would be directly applicable to searches for general area cladograms However to avoid conflicting dispersal events cf Fig 3 one would have to search for an optimal solution not only in the universe of all possible area cladograms but in the universe of all possible time segmented area cladograms Since there is one possible time segmentation for each sequence of speciation events i e sequence of vicariance events and there may be many possible sequences of speciation events for each cladogram Fig 6 this universe is considerably larger than the universe of all
41. st matrices In the future we will undoubtedly see more sophisticated uses of three and two dimensional step matrices in coevolution and historical biogeography An important challenge in historical biogeography will be to incorporate geological constraints into the model such that reticulate and hierarchic biogeographic scenarios can be tested directly against each other on equivalent terms Some pitfalls in dispersal vicariance optimisation Ancestral areas When using DIVA to reconstruct the ancestral area or centre of origin of a group of organisms Bremer 1992 it is important to remember that optimisations become less reliable as you approach the root node This is because the tree that you work with represents a small part of the tree of life and the globally optimal states of the basal nodes in your subtree are particularly heavily influenced by the rest of the tree of life The root node state i e the ancestral distribution is the least reliable in your entire tree In DIVA this uncertainty will be manifested as a tendency for the root node distribution to be large and include most or all of the areas occupied by the terminals If you are interested in more reliable estimates of the distribution of the root node you should include additional outgroups in the analysis such that the node is no longer the root node Alternatively it might be useful to examine the effects of imposing constraints on the maximum number of unit areas allowed
42. t F and S Nylin 1990 Process and pattern in the evolution of species associations Syst Zool 39 323 344 Swofford D L and G J Olsen 1992 Phylogeny reconstruction In Molecular systematics edited by D M Hillis and C Moritz Sinauer Sunderland Wiley E O 1988 Parsimony analysis and vicariance biogeography Syst Zool 37 271 290 Department of Systematic Zoology Latest update 02 2001 WebMaster http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 21 of 21 Uppsala University O Department of Systematic Zoology m DIVA Manual http www ebc uu se systzoo research diva manual dmanual html 30 03 2009
43. t to restrict the number of alternative distributions kept at each node with the keep option of the opimize command An alternative is to restrict the number of unit areas allowed in ancestral distributions using the maxareas option The smaller the maxareas value the faster the optimisation Once the length of one reconstruction is known this value can be used as a bound in an unconstrained search using the bound option of the optimize command Unfortunately the amount of time saved by improving the bound may be insignificant in many cases Entering commands Commands can be entered from the keyboard or processed in a batch file DIVA uses its own format for batch files but it can also process NEXUS files Normally you will prepare a batch file minimally containing a tree description and a distribution specification A good way of creating this batch file is to use MacClade see the next section for detailed instructions The character matrix should then be a distribution matrix Fig 4 recording the presence 1 or absence 0 in the areas being considered More laborious tasks can be accomplished by preparing a text only batch file with your favourite word processor and then run it in DIVA with the proc command The batch file must be in the same folder as DIVA http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 12 of 21 Comments can be included in a batch file as lines starting wit
44. tion parasites adding a new host parasites species to the range of hosts attacked Successive specialisation narrowing of the association after speciation to include b fewer members http www ebc uu se systzoo research diva manual dmanual html 30 03 2009 DIVA 1 1 User s Manual Page 3 of 21 The basic idea was to use cost matrix optimisation to reconstruct the history of associations Ronquist and Nylin 1990 To do that it is necessary to specify a relative cost for each of the events in the model the cost being inversely related to the likelihood of the event occurring Once the costs have been determined it is possible to find the minimum cost reconstruction which would be the most likely most parsimonious or maximum likelihood explanation for the origin of the pattern being analysed Ronquist and Nylin focused on systems where the sets of associated species were determined by parasite and host traits active associations If these traits remained unchanged host or parasite speciation would result in duplication i e broadening of the association to include more members Thus duplications may be considered the null model in coevolutionary inference and associated with a cost of zero just like maintenance of a trait no change is the null expectation in ordinary parsimony optimisation of morphological characters To simplify the problem further Ronquist and Nylin introduced the assumption that each parasite occupie
45. which the optimal distribution is ambiguous will be included in summary statistics Default setting is to include ambiguous ancestral distributions relative absolute Determines the type of time classes used Absolute time classes are defined by the number of speciations separating ancestral nodes from terminals Relative time classes are defined by the ratio between the number of speciations for an ancestral node and the number of speciations for the deepest node in the cladogram multiplied by the age of the group The default setting is absolute classes x Defines the number of time classes used The number must be smaller than or equal to 5 The default value is 1 interval x Sets the width of the time classes except the oldest one If absolute is specified the value must be an integer Default setting is 5 for absolute time classes and 0 5 for relative time classes bounds n x1 x2 xn Allows the user to specify time classes of unequal size The number of bounds is specified by an integer n Following this is a list of integer or floating point numbers x etc specifying the upper bound of all classes except the oldest one If bounds are not given for all classes the interval value is used to obtain the missing bound values sumareas x Constrains the summation to only consider the first x areas The value of x must be in the range from 0 to 8 The default value is 0 no information summarized return Used at the end of a b
46. zation to x which must be between 0 and 1 The weight is used in the calculation of summary statistics The default value is 1 0 printrecs Prints all alternative equally optimal reconstructions If printrecs is not requested output is restricted to a summary of the optimal most parsimonious distributions at each node output filename Redirects output to the specified file The file will be created in the same folder as DIVA DIVA can only create new files it cannot overwrite or append to existing files The setting of echo determines whether the output will be echoed to screen If filename is the output file is closed and output is redirected to the screen console proc filename Changes control from screen to the batch file named filename The batch file must specify a series of commands as they would have been typed in from the keyboard It must be a text file and it must be in the same folder as DIVA unless a correct file path is specified Control is returned to the screen console when proc or return is encountered or when the end of the file is reached A batch file cannot be created in DIVA Instead you will have to use a word processing program and save the file in text only format The proc command can also be used to process NEXUS files containing a presence absence distribution matrix and a tree specification If the NEXUS file contains several tree descriptions only the last will be retained by D
Download Pdf Manuals
Related Search