VIP: Vicariance Inference Program Version 10.02.15 by J. Salvador
Contents
1. Also it is possible to compile the code yourself The source is write on plain C using gtk Make sure you have the latest version of gtk dev library available here http www gtk org download html linux users can download and install it with synaptic app get or a similar application In windows you need to link the program including the following libraries gdk win32 lib gdk_pixbux lib and pango lib 1 5 License and citation The source code of vip and its documentation is distributed with a creative commons license source GPL http creativecommons org licenses GPL 2 0 documentation attribution share alike http creativecommons org licenses by sa 3 0 which means that you can use and modified it as long as you give attribution and keep the same license As any scientific work if you use this program please cite the method description 5 Hovenkamp original proposal 3 4 and the program itself Also suggest including algorithms or methods used modified by the program such as 8 and 11 where applicable 1 6 Contact will be happy to hear you for any questions suggestions bug reports your vip user experience or your code modifications You can contact me at jsalarias csnat unt edu ar If you like also can include you in a list of vip users so can send you reminders of new available versions For bug reports please specify how the bug is triggered and if possible a data set that produce the error Als2. that did not pertains to the reconstruction are showed as void boxes If unchecked just the records assigned to the actual reconstruction are showed 9 3 Barrier Ctrl B If checked shows the potential barrier associated with the selected node if the node is reconstructed as vicariant see Barriers menu 9 4 Grid Ctrl G If checked display the grid based on the actual grid settings 10 Barrier operations Map Window gt Barriers This menu is active only when the barrier option Map Window gt Drawing gt Barrier is checked It change the display and properties of barrier drawing Barriers are calculated using the Voronoi Delaunay dual graph on the records reconstructed for the selected node But instead of storing all triangles cells just the triangles that contain points from each descendant are kept Points on overlapping areas are not taken into account for the triangulation KNOWN BUG This is not exactly a bug just a consequence on how the program works i e assuming a limited earth For some amphi pacific distributions triangles connecting both pacific halves are never searched 10 1 Voronoi lines Ctrl V When this option is selected a line using the Voronoi tessellation is showed Note that the line did not necessary fall in the correct barrier it is only a devise to easily locate the potential geographic barrier associated with the disjuntion As the Voronoi segments are mid distance lines farther po
3. ties slow down the search and it might fall to found reconstructions as the search get stuck at ties If there are already reconstructions in memory checking keep actual reconstructions check box do not clean the reconstruction buffer before the search and the best score of the actual reconstructions is used as bound Note that if a better score is found then the buffer clean all reconstructions as they are suboptimal When a search is performed a progress dialog shows the status of the seach KNOWN BUG When the search is about to finish some times very few the progress dialog suddenly show an extraneous number if numbers are shown and freezes Actually the search was finished and results are displayed on screen but the program fail to close the dialog If you suspect that the search takes longer than expected and the progress bar is just near to the end try to close the dialog if it not close then the search is already running This error is very rare 5 2 Consensus Ctrl C After a search the consensus of the found reconstructions can be calculated Note that before each search the consensus is cleaned After every search consensus is only calculated the first time that this menu or the consensus reconstruction option on reconstruction flap is selected any other selection of this options just shows the previous consensus 5 3 Filter Ctrl F Removed all suboptimal reconstructions and clean the consensus It can be he
4. VIP Vicariance Inference Program Version 10 02 15 by J Salvador Arias User s manual Index 1 Introduction The biogeographical analysis within a single lineages taxon history has been subject of several methods based on the concept of ancestral areas e g Fitch optimization 1 or DIVA 2 Unfortunately such methods rest on the idea of predefined areas that are optimized in some way into a phylogenetic trees There are several problems on the use of predefined areas 3 4 that ultimately end in the doubtful implementation of such methods 5 Based on insights from Rosen 6 Hovenkamp 3 4 propose a method to deal directly with spatial data in a phylogenetic context Although his objective is more akin to cladistic biogeography a search for history of earth ideas from Hovenkamp are useful for use in taxon history The program present here Vip uses ideas the ideas of Hovenkamp in a optimality criterion framework allowing the user to set reconstruction costs use heuristic searches and visualize the results in a geographical defined graphic interface 1 1 Data requirements Vip requires two types of primary information First it requires a cladogram depicting phylogenetic relationships among the study taxa The second type of data is georeferences latitude longitude from terminals Each terminal must have a georeferenced point to be taken into account in the analysis Additionally in the case of time calibrated phyl
5. al 5 degree cell for each record 4 2 Create grid Ctrl A The grid set does not creates the grid just set the rules for the grid creation The create grid menu creates a grid in memory As the grid is compressed to save memory and computation time record edition is unavailable after the grid is created When the grid is created a default OR reconstruction is performed on the data activating several of the information boxes in the reconstruction tab 4 3 Destroy Grid Ctrl D Removes the grid and the reconstructions from memory The absense of grid is reflected on reconstruction tab showing no grid in several fields As the grid is removed it is possible to edit records 5 Reconstruction operations Main Window gt Recons menu This is the basic menu of Vip It encapsulates the basic operations about reconstructions searching consensus and filtering reconstructions 5 1 Search Execute Ctrl E This menu displays the search dialog The search use an iterative removal 5 8 of nodes to search for the best reconstruction score for details see 5 The dialog display the number of independent iterations by default 100 Accept equals box is used to stipulate the frequency in percent units to keep ties at each iteration by default it is 50 A low or 0 value of this parameter make the search faster but for typical data this setting surely fails to even hit the best score With values near to 100 i e accept nearly all
6. ates lt coordinates gt using longitude and latitude Here is an example lt Folder gt lt name gt Bassaris_itea lt name gt lt Placemark gt lt Point gt lt coordinates gt 145 5000 20 0000 lt coordinates gt lt Point gt lt Placemark gt lt Placemark gt lt Point gt lt coordinates gt 168 0000 45 0000 lt coordinates gt lt Point gt lt Placemark gt lt Folder gt 3 3 Save Ctrl Shift S It is possible to save files using pkml format for example after edition or a kml file to be open with Google earth 3 4 Close Ctrl W This option removes all the loaded data from memory without closing the program 3 5 Quit Ctrl Q Exit the program 4 Grid operations Main Window gt Grid menu Vip uses a grid to represent the spatial distribution of taxa The grid menu is used to set the basic properties of the grid 4 1 Set grid Ctrl G This menu sets the size of each grid and the filling around The grid always start at 180 lon 90 lat The fill is the number of cells around the record to be counted as presences For example a fill of 0 only the cells in which a record fall are counted with a presence a fill of 1 the eight cells surrounded the cell in which the record fall as presences Instead of trying several starting points of the grid it is better to use an small grid size and a fill For example instead of a 5 degree cells using a 1 66 degree cells and a fill of 1 make a virtu
7. aximum vicariance 7 8 9 If removal has an infinite cost the result is the maximum number of possible nodes explained without removal as in the original Hovenkamp s method 3 4 and similar to assumption 0 3 or paralogy free subtrees 10 Details about the method are described in 5 1 3 Results The results of an analysis with vip is displayed in two windows the map and the tree window In the map window allopatric distributions are displayed using red and blue for each descendant if there are some overlap it is show in green It is possible to show a potential barrier calculated using the Voronoi tessellation In a tree window nodes with allopatric distribution are marked with a black square Nodes with removed distributions are shown as white circles In some cases a node is removed but it also has an allopatric distribution in such cases a white square is displayed in the node 1 4 Running VIP Vip can be downloaded as binary or in form of source code Binaries for Linux and Windows are available 1 4 1 Linux binaries To run linux version you need to install the gtk bin package This package is already installed in Gnome desktop For KDE you can install this package using synaptic get app or a similar tool from your preferred repository 1 4 2 Windows binaries To run the program you must install the gtk windows runtime The latest version can be downloaded here http sourceforge projects gtk win
8. f the mouse window there is a label showing the latitude and longitude at the mouse pointer if it is on the map 3 File operations Main Window gt File menu Basic file operations are packed in the File menu at Main Window this operations behave nearly identical to file operations in most GUI applications 3 1 Open Ctrl O This menu shows a file chooser dialog that allows the user to select a file to be open At this moment the only valid format is the pKML files KML like files Although just only one file can be open each time several files might be open allowing the user to use multiple trees 3 2 Format input The pKML files are a derivation of the KML files used by Google Earth Although not any KML file can be easily transformed into a KML file the pKML files are nearly compatible with the KML standard It is not expected that the user edit directly this files A simple TNT macro is provided topkml run to write a phylogenetic tree into a pkml file Then using vip the point localities of each terminal can be inputted manually All pKML files start with a lt Document gt token a name between lt name gt and lt name gt is optional Each node internal or terminal must be identified with the lt Folder gt token If it is a terminal the folder can contain one of several lt Placemark gt To close a node the token lt Folder gt is used The lt Placemark gt token identified a point lt Point gt and its coordin
9. he menu Recons Search and perform the search using the actual parameters equivalent to apply and then search The reconstruction tab is used to show some basic statistics of the actual reconstruction and to navigate across the data The tree navigator shows the number of trees in memory and the name of the actual tree With the buttons back and forward is possible to change the tree The reconstruction navigation box shows a cost box with the actual cost of the reconstruction the vicariant box show the number of vicariant nodes in the reconstruction the box nodes with removal indicates the number of nodes with a removed distribution The reconstructions in memory shows the number of reconstructions found with the searches and if a searched reconstruction is selected indicates the id number of the actual reconstruction in this case the back and forward button allows the user to change the reconstruction The option entries OR reconstruction Searched reconstruction and Consensus reconstruction are used to select among reconstruction kinds The node navigator shows the label of the actual node it can be changed using the back and forward buttons 2 2 Tree view window The tree view window is used to visualize the actual tree and the reconstructions if any To move the tree inside the window it is possible to use arrow keys or holding the mouse left button drag also if there are a mouse wheel it can be used to scroll the tree ver
10. ints produce less meaningful barriers KNOWN BUG In some reconstructions for a problem in the sorting of triangles in some drawings a loop is displayed These loops are easily identified and apart of unpleasant aesthetics they are harmless 10 2 Delaunay trinangles Ctrl D When this option is selected the triangles of the Delaunay triangulation are showed This is equivalent to show the space between the disjoint distributions 10 3 Barriers on ancestors Ctrl N If checked display the barriers detected on parent nodes of the selected node The ancestral barriers are displayed as broken and slim lines 10 4 Common barriers Ctrl I If checked and a consensus reconstruction is selected it display the barrier associate with the common allopatric set associated with the node see under Tree window gt Reconstruction menu as a thin line It uses a very conservative procedure using the disjunctions associated with all nodes in the allopatric set even if these nodes are not simultaneously supported References 1 Fitch 1971 2 Ronquist 1997 3 Hovenkamp 1997 4 Hovenkamp 2001 5 Arias et al ms 6 Rosen classic 7 Page 1994a Component 8 Page 1994b Tree map 9 Ronquist 1999 libro 10 Nelson amp Ladiges 1996 11 Upchurch amp Hunn chronobiogeography 12 Arias in prep
11. lpful for example how is the best reconstruction found under other cost parameter setting 5 4 Clean Ctrl L Removes all reconstructions in memory 6 Edit operations Main Window gt Edit menu This menu contains some basic edition options This instructions are only available under certain circumstances 6 1 Hot mouse Ctrl H Checking this option allows the user to edit manually the records for each terminal It is only active when there are no active grid A terminal must be selected Records can be added on the map window by pressing the right mouse button holding the shift key By clicking the right mouse button and holding the Ctrl key over a record a georeference browser dialog is displayed showing the selected point it is possible to change the coordinates or delete records using this dialog box 6 2 Edit reconstruction Ctrl T When a searched reconstruction is selected pressing the right mouse button holding the Ctrl key over a node in the tree window change its status removed or not removed and vice verse Two points must to be taken into account First the selected recostruction is lost and second partial overlapping is not calculated so if the changed node has some partial removal this information is lost 6 3 Georeference browser Displays the georeference browser If the grid is not active and Hot mouse option is selected is possible to edit georeferenced records 7 Tree formating Tree window g
12. o will be happy if you send me a pdf copy of your published results using vip 2 General layout Vip is a program that uses a Graphic User Interfaz GUI based on different windows There are three basic windows The main window has the menus and parameter entries for basic operations such as data loading searches reconstructions and data edition The tree window displayed the actual tree and node it has menus for basic tree display The map window displayed the position of records for the selected node and a map if any it has menus for map configuration and record display In all windows there are keyboard shortcuts for all menu operations In this section a general overview of the layout is provided more detailed accounts based mostly on menu actions are given in the following chapters 2 1 Main Window The main window is used for user input files and search reconstruction parameters and for a basic report of the results It has four menus File menu is similar to most program s file menu it is used to load input data export data and exit the program Grid menu is activated when there are some data it is used to set the grid Recons menu is activated when a grid is active it is used for searches and reconstruction operations Edit menu is activated when there some data it is used to some basic edit operations for the records and reconstructions The windows has two tabs The first tab is label as parameters It is used t
13. o set the parameters used during the reconstruction The box cost of non vicariant nodes is used to set cost of nodes that are not allopatric The box cost of node removal is used to set the cost of a distribution removal The cost of the reconstruction is the sum of the cost assigned to each node The check box use fractional cost is used to give more grain to the reconstruction If fractional costs are used then an allopatric node might be with a cost if it has some overlapping the cost is proportional to the overlap cost non vicariant cost overlap ratio for example with a cost of 2 0 and an overlap of the 10 the cost of the node is 2 0 0 1 0 2 The max overlap box sets the maximum as percentage acceptable overlap for a node to be counted as allopatric The late overlap box allow the program to search using late overlap that is instances of overlapping in a nested node with respect to a node attached more basally see 5 The max late overlap box is used to set the maximum late overlap acceptable If late overlap and fractional costs are used simultaneously then the removal cost is scaled with the overlap ratio If data is time calibrated then the use time check box is activated With this option checked the searches take into account the age difference between the descendants similar to 11 see 12 Apply and cancel buttons are used to set the values or the return to the previous ones Execute button is equivalent to t
14. ogenies i e an analysis including fossils is possible to assign an age to terminals and nodes A detailed account on data formats and data edition can be found in the following sections 1 2 Program background Hovenkamp 3 4 argued that the only evidence left from an speciation process in a geographic context are allopatric distributions Unfortunately although many clades show an allopatric distribution many does not There are some distributions that present some form of overlap others in that a widespread terminal or clade make uninformative several of its ancestral nodes Some of these problems are also found in the area based biogeography Area based biogeography assumes that distributions can be resumed as few homogeneous areas Vip does not take that approximation but it uses some solutions developed under such paradigm 7 8 If a distribution of a node is ignored and it is possible to found a solution with more nodes showing allopatric distributions this solution might be preferred as it increases the explanatory power of allopatry But also removing a node is a form of an ad hoc rejection of conflicting evidence Vip uses a system of costs in which the user can set the cost of a node distribution removal and the cost of a non vicariant node a node that can not be explained geographically If distribution removal has a cost of 0 the result if the maximum number of possible nodes explained by allopatry that is m
15. struction off all nodes that share a common allopatric pattern with another node Note that given the nature of the set reconstruction the showed node might not be simultaneously supported 8 Map operations Map Window gt Map menu This menu is used to basic map operations such as loading and scale 8 1 Open Ctrl O Load an image to be used as map Most popular graphic formats as jpg gif bmp and png are supported The map must be in a cilindrical and isometric projection i e equirectangular projection to coincide with the window coordinate system 8 2 Map limits Ctrl L This menu display a map limit dialog It is used to set the limits of the actual map so the map will be put on the right coordinates and in adequate the scale Note that the limits are just for the loaded image Records can be scattered in any valid geographic point of the earth In absence of loaded image it can be used to change the scale of the displaying window it is assumed than an image of 720 x 360 pixels is loaded 8 3 Centre on Ctrl C Center the window at the selected coordinates 9 Drawing operations Map Window gt Drawing menu This menu is used to change the display on the map 9 1 Record radius Ctrl R Allows the user to change the size used to draw records The radius is measured in pixels It also change the mouse radius sensibility above records 9 2 All records Ctrl A If checked the default shows all records records
16. t Format menu This menu allows the user to configure the shape and sorting of the tree If the tree contains time labels it is possible to draw the tree as a chrono tree Ctrl C in which branch forks are displayed according to their associated time 7 Tree reconstruction operations Tree window gt Reconstruction menu This menu is used to show reconstructions when the consensus reconstruction is selected After making the consensus the program check if there are other available nodes that share the same vicariant distribution than the selected node To be available a node must be on an independent clade to the selected node i e it can not be a descendant or an ancestor This is equivalent to search for a supported vicariance event But different from 3 the search is node based so instead of finding an event it find other nodes that share a common allopatric pattern with the selected node This in that sets might be no reciprocal For example a node A share an allopatric pattern with node B and node C but node C is a descendant of B so node C will not be valid on the common allopatric set of B 7 1 All reconstructions Ctrl L The default option shows the reconstruction of all nodes 7 2 Common reconstructions Ctrl N This option shows only the reconstructions that share the same common allopatric pattern as the selected node 7 3 Supported reconstructions Ctrl S This options shows only the recon
17. tically Tree size can be changed with arrows keys and Ctrl button To quick size Ctrl F fit the tree to the actual window and with Ctrl T fit the space between terminals to be readable With the mouse left button is possible to select nodes by a click Also using page up and page down the selected node change The selected node is marked with a green square If the node is a vicariant node then their descendants are marked with a red and blue square With a click of the right button information about the node is displayed and the name of the node can be edited If there are a reconstruction then the vicariant nodes are displayed as black squares If the node span is removed is displayed with a white circle If the node span is removed but also is a vicariant node then it is show with a white square 2 3 Map window The map window is used to display the records of the selected node The records are displayed as green squares If the node is a vicariant node then the records of each descendant are displayed in red and blue according to each descendant in coordination with the colors used in the tree view window in such cases the overlap is show in green In the case of consensus reconstructions not all records are included so they are showed in white With a click on the left button of mouse over a record information of the particular record is displayed By holding the right button it is possible to move the map At the bottom o
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