User manual
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1. Borttaget TRL 12 6 4 3 Click on Group Analysis The analysis will be run and the results will be copied to the Clipboard Open an empty Excel sheet and select Edit Paste or Ctrl V to paste the Clipboard data into Excel Save the Excel file SEEYA v0 33 Einar Heiberg 2008 E mi fe x Fie Tree Help Open Data File TachiaRAWDATA xls Store Messages to File Finish Writing Messages m Manual Analysis gt Group 1 grandifolia gt Group 2 guianensis longipes orientalis gt Group 3 gt Group 4 gt Group 5 Clear groups D e eoe Data columns Group Analysis Tree Analysis Load Tree TachiaMATRIXTREE nex Plot Tree Tree Analysis Fig 7 The user interface when you have loaded a Data file a Tree File and selected species for your Manual Analysis and selected 4 variables for analysis 6 5 Comparison of species based on a phylogenetic tree 6 5 1 Select Load tree in the Tree menu 6 5 2 To see the tree use Plot Tree in the Tree menu This tree can be printed to a printer or a pdf file if you have Adobe Acrobat or Distiller and you can also zoom the tree under Print Preview Nodes are indicated with numbers 6 5 3 Select one to several data columns for the variables you want to analyze 6 5 4 Under Tree menu select Analyze tree You will be prompted to save the results in a new Excel file You cannot add data to an existing Excel file so give each re2. gathered from species or individuals in a spatial taxonomic and or phylogenetic context using the Spatial Evolutionary and Ecological Vicariance Analysis SEEVA methodology developed by Lena Struwe Richard Lathrop and Scott Haag Peter Smouse at Rutgers University USA and Einar Heiberg at Lund s University Sweden geography Fig 1 Showing the complex interaction between geography distribution space phylogeny evolution ancestry and ecology environment climate through time for a lineage In contrast to traditional vicariance biogeography which assumes geographic separation of populations the Spatial Evolutionary and Ecological Vicariance Analysis approach allows researchers to look at ecological vicariance differences of sympatric and allopatric species and clades This method can utilize GIS derived dataset of collection associated ecological and environmental data in combination with phylogenetic data to investigate trends in speciation using statistical methods with spatial interpretations The method can also be used for many other kinds of comparisons between groups and clades in areas such as co evolution diseases morphological evolution and niche comparisons Generally SEEVA works by using measurements gathered from individuals of species or populations and these measurements are then analyzed statistically for differences between groups species and or clades Two statistical test have been employed the chi
3. is written in Matlab For you who do not have Matlab we have compiled the application to a stand alone application so it can be run on any Windows computer If you want to run the software on other platforms such as Mac or Linux please contact the Einar Heiberg and you will then be provided with the source code so the software can be run from Matlab on that particular platform The precompiled version runs on PC under Windows XP Vista NT ME but this program does not work on Windows 98 You will need 500 MB free harddrive space and 256 MB RAM memory 1 Install Matlab Component Runtime First a program called Matlab Component Runtime is required This is essentially a small Matlab installation but can only be used to run precompiled applications If Matlab Component Runtime is already installed you can omit this step but double check your version This is found in Windows control panel under Add Remove programs Look for MATLAB Component Runtime 7 8 on the list size 466 MB If your Matlab Component Runtime version is less than 7 6 then you need to uninstall the old first and then install the new program see under 1 2 below Uninstalling the old one is done by clicking on its name in the list and select Remove You need to be logged in as an administrator to do this 1 1 Log in as administrator on your computer 1 2 Download the file MCRInstaller_R2008a exe large file 200 MB from http seeva heiberg se 1 3 Install Matlab C
4. square test and Fisher s Exact test the latter to provide a better p value for tests with small sample sizes Environmental variables are divided into categories either as non ordered qualitative sections e g soil types or ordered quantitative sections representing quartiles of the total amount of data e g precipitation categories A statistical test is performed to investigate if the distribution of species or monophyletic clades in different categories of environmental variables shows a random or non random pattern with taxonomic group vs counts for collections for the categories for one variable in an X x Y multi way table number of variable category 2 category 3 category 4 observations category 1 species clade A 0 10 16 21 species clade B 10 15 9 0 Table 1 Example of X x Y multi way table showing skewed character state distributions for two different groups using 4 states for one particular variable The numbers are number of observations i e collections A non random skewed pattern a stronger association for an environmental character state s with a specific group clade both historically evolutionary and presently The classification of the environmental variables is rather coarse but these tests provide a way of looking for broad patterns Examples of questions that can be analyzed with the SEEVA method include e Which environmental variable show the biggest difference between two siste
5. MANUAL SEEVA Software Spatial Evolutionary and Ecological Vicariance Analysis Beta version ver 0 33 released Nov 1 2008 By Einar Heiberg amp Lena Struwe websites seeva heiberg se or www tci rutgers edu struwe seeva Important note This software is a work in progress and the full version not yet released We appreciate any feedback and suggestions for improvement SEEVA is a free software product to all non commercial and academic users If you are a commercial user private company or similar please contact us for licensing fees 2008 Einar Heiberg amp Lena Struwe All rights reserved einar heiberg se struwe aesop rutgers edu How to cite the SEEVA methodology Struwe L P Smouse S Haag E Heiberg amp R G Lathrop Manuscript SEEVA Spatial Evolutionary and Ecological Vicariance Analysis a new interdisciplinary approach to historical biogeography and niche changes J Biogeography to be submitted How to cite the software Heiberg E 2008 SEEVA ver 0 33 Software for Spatial Evolutionary and Ecological Vicariance Analysis Available from the author at http seeva heiberg se How to cite the manual Heiberg E amp L Struwe 2008 SEEVA manual On line publication Rutgers University Available at http seeva heiberg se and http www rci rutgers edu struwe seeval Introduction and Methodology This software package authored by Einar Heiberg www heiberg se processes data
6. STreeAnalysis xls Results File comments added Macrocarpaea 62 species including outgroups MacrocarpaeaRAWDATA xls Data File environmental data for 800 collections and 5 variables 1 quantitative 4 qualitative as well as collection ID numbers and geolocation data MacrocarpaeaMATRIXTREE nex Tree File datamatrix and tree file in Nexus format MacrocarpaeaRESULTSManualAnalysis xls Results File MacrocarpaeaRESULTSTreeAnalysis xls Results File 14 Known issues Under certain circumstances the calculation of exact p value for Fisher Exact test fails This happens particularly when calculating larger polytomies To proceed with the calculation press the OK button When this happens no value for p value is provided for that node In most cases you can then safely use the chi2 p value instead since this happens when the number of items is relatively large Mailing list Join the SEEVA mailing list for information about updates and new versions Subscribe here https email rutgers edu mailman listinfo seeva_list 2008 All rights reserved Einar Heiberg amp Lena Struwe einar heiberg se struwe aesop rutgers edu
7. be modified by you in the Excel sheet to include a minimum of two and a maximum of four states each with each state not being a number A B C is OK but 1 2 3 will not work because if numerical SEEVA will treat the data as quantitative You can have longer descriptions as well such as forest savanna The program only reads the first sheet in the Excel workbook Please see example files Empty cells are permitted and will be treated as a non existing value and will be excluded from the analysis Note For numeric variables they are automatically divided into quartiles The ranges of the quartiles are printed above all node comparisons in the output file see below In future versions of the program these limits will be possible to encode manually 4 Prepare the tree file if needed A tree file is necessary if you want to base your analysis on topologies and comparisons of node by node patterns If you want to compare 2 5 groups taxa without any particular topology you can do a manual analysis without a tree file The tree file should be in the NEXUS format and end with nex text only file You can have several trees in your treefile but you can only analyze one at the time in SEEVA Polytomies in the trees are allowed but will affect your statistical analysis since you will have more groups to compare Note Taxon names in the tree file must correspond exactly to the Excel sheet s species name column Root or orie
8. ble is minimum Tree Analysis Load Tree Loads tree file Plot Tree Shows tree 11 Analyze Tree Runs SEEVA analysis of all nodes in a tree for the variables that have been selected Note The number of variables that can be analyzed simultaneously are dependent on 1 how many columns you can fit into the Excel Results sheet and 2 your computer s RAM memory We have successfully run analyses with up to 10 variables at the time You can analyze your variables in batches and then combine the results in Excel for a complete overview io xi File Cae Saar ea e 08 Fig 6 Example of Tree shown inside SEEVA Numbers refer to each node s number 6 4 Manual comparison of species Group Analysis 6 4 1 In the Species window select species to compare Select several species for one group by holding down the Shift or Ctrl key All species for a group has to be selected at the same Borttaget SHIFT time Click on Group 1 to set the first grouping on group 2 to set the second grouping The Borttaget TRL output result will list which species that are member of what group Currently you can not analyze more than 5 different groups against each other Clear groups deletes your selection of taxa so you can start over 6 4 2 Select the Data Column name of the variable to be analyzed by clicking on the name of the variable you can select several use Shift or Ctrl Borttaget HIFT
9. ental variables as shown by non random associations of particular species or clades and their environmental situations It should not be assumed that environmental variables are independent in fact many of them are not and an assumption of independency is not necessary for this analysis Borttaget w Senaea jeneirensis S caerulea Prepusa montana P viridiflora P data P hookeriana P connata SOIL TYPES m chromic cambisols red brown and brown dry savanna umbric ferrisols ferralitic and allitic rich in humus eutric cambisols subtropical and tropical brown forest soils eutric cambisols brown forest soils cold temperate areas Fig 2 Differences in distribution of 4 soil categories one variable throughout a phylogenetic tree The numbers are impact indices for each node the bars indicate percentage of categories present in each sister group The figure was Borttaget r made in Powerpoint with customized graphs imported from Excel Senaea janeirensis S caerulea Prepusa montana P wiridiflora P data P hookeriana P connata mm Soil type mm Temperature Seasonality mm Minimum Temperature Driest Quarter Precipitation Seasonality w Annual Precipitation mm Elevation Fig 3 Differences in impact indices for 7 environmental variables throughout a phylogenetic tree Download and Installation download website http seeva heiberg se The SEEVA program
10. es in the sister clades and one variable showing to the right the character state distributions for two clades and their observed data colletions then to the left the P value from the chi square analysis the degrees of freedom and the impact index number all from the SEEVA analysis Note that in this particular case a Fisher s Exact analysis is needed to get an appropriate p value since the sample sizes are so small 3 0 43033 The species can be grouped in two ways for the SEEVA analysis 1 species by species Manual Analysis and 2 by sister clades Tree based The latter approach includes phylogenetic information since species data from two or more if a polytomy clades will be compared and analyzed and environmental trends and reactions over the time of the evolution of a group can be assessed by comparing impact values between nodes Caveats and notes The method works with a minimum of one record for each species however results based on such a small sample should be evaluated with caution In general correlations between divergence and environmental variables can be inferred as trends and tendencies within phylogenetic lineages and not as the definite cause for the divergence until further research The generic null hypothesis for all tests is that the cross classified factors are completely independent and the hypothesis driving the work is that Species or clade distributions are influenced by specific environm
11. g down the Shift or Ctrl keys 10 SEEYA v0 33 Einar Heiberg 2008 p 5 x Fie Tree Help Open Data File Macrocarpaea xis Store Messages to File Finish Writing Messages m Manual Analysis gt Group 1 gt Group 2 gt Group 3 gt Group 4 gt Group 5 Clear groups Group Analysis Tree Analysis Load Tree Macrocarpaea nex Plot Tree Species Data columns IGEOLOGIC_AGE il Tree Analysis Fig 5 The user interface when you have opened a data file 6 3 Overview of windows interface and options Menu options File open and clear data file quit Tree open analyze and plot tree Help Home page About Submit bug report Buttons Open Data File Opens Excel sheet with data Store Messages to File Opens a log file for error messages and run commands This is helpful for troubleshooting Finish Writing Messages Closes log file Windows Species Species names pulled from Excel data file Data columns Lists columns of variables pulled from the data file listed in order from left to right in the data file Manual Analysis Group 1 5 Add species to each group as you want hold shift or Ctrl key to select more than one species at a time Select all species you want first then add them or the selection will overwrite the previous selection Select variables to analyze in right window Click Manual analysis to compare at least 2 groups are needed one varia
12. nt your tree before importing it into SEEVA You will not be able to reroot it inside SEEVA 5 Example and template files One large Macrocarpaea 50 species and one small Tachia 13 species example files are provided as templates and can be downloaded on the SEEVA websites Note that this data does not reflect actual scientific data and phylogenetic hypotheses These data matrices are only templates for formatting training and testing by the SEEVA users None of the data is published or accurate More details about the template example files are given later in this manual Kommentar A1 Have you tried with more I have no recollection of minimizing to 4 Borttaget Borttaget Also sometimes Running SEEVA 6 Run SEEVA 6 1 Double click on seeva exe to start SEEVA If you get a warning about the publisher being unknown ignore this and click OK SEEYA v0 33 Einar Heiberg 2008 Iree Analysis Fig 4 The user interface when you open SEEVA 6 2 Load Data File and Tree File the latter is optional Click on Open Data file pushbutton to select a data file to load To load a tree select Load Tree in the Tree Analysis panel This step is only required if you intend to run a tree phylogeny based analysis If the tree file contains more than one tree then you will be prompted and can select which tree to import Species and variables can be selected by clicking the mouse and holdin
13. omponent Runtime MCRInstaller_R2008a exe by double clicking on its icon If the program asks you to install VCRedist_x86 as part of this installation this is OK 2 Download SEEVA 2 1 Download the file seeva exe from http seeva heiberg se 2 2 Create a new folder we suggest the name SEEVA on your computer and place the file seeva exe in that folder Preparing the data files 3 Prepare Excel file with variables Prepare an Excel file that has one column named SPECIES which will contain the taxon name for each collection For each collection add environmental data either as quantitative measurements elevation etc or qualitative vegetation type We used geolocated specimens and ArcGIS to pull out environmental data from many base layers of data from sources such as USGS WORLDCLIM etc The species column has to be to the left of the columns with variables you want to analyze You can have additional columns with other data such as collection ID geolocation etc and this will not affect the analysis The top row is the name of each column Do not have empty rows or columns inside you spreadsheet but you can have empty cells for missing data Borttaget Mb Quantitative data will be divided up automatically in four groups from min to max in SEEVA with borders between categories currently defined so one fourth of all samples are in each category to optimize repeatability Qualitative variables has to
14. r groups or two sympatric species What patterns in soil types do you see as you move up in the phylogeny of a group Are species in dry season areas derived from wet season areas Is long distance dispersal associated with changes in ecological traits What came first higher rainfall or higher elevation in a particular clade Do allopatric sister species show larger ecological divergence than sympatric sister species The SEEVA method can be enhanced when combined with dispersal vicariance analysis DIVA ancestral area analysis dating methods geographic mapping of populations endangered species analysis and ecological niche analysis The method will work on any kind of data including absence presence of diseases morphological or phytochemical measurements pollinator type color morphs as long as individuals are measured Using the chi square value an impact index i that is independent of sample size and degrees of freedom is being calculated i square root of chi square value df x sample size N This index provides a measurement for the skewness for each node and variable and therefore a possibility to compare different nodes and different variables species clade p chi2 df impact index category category category category 4 viridiflora 0 0 0 0 093473 2 alata hookeriana connata Table 2 Example of results table for one node with one species vs 3 speci
15. sults file a new name 6 6 Understanding the data output Open Excel and the results file The setup of the results file is the same for Manual Analysis as for Tree Analysis 13 E3 Microsoft Excel Book1 loj x H File Edit Yiew Insert Format Tools Data Window Help Adobe PDF 8 X Pl 275 OS i ig iQ ara z110 He 77 te ES os Rad sad eel noe oe K11 S fe A Variable YWEGETATION_TYPE text in red added for explanation not part of results output above name of variable below category 1 category 2 category 3 TotChi2 NormChi2 pchi2 df impact fac p clade 1 2 5 clade2 gracilis lore 72 62 2 p value p value gt Pi Sheet1 Sheet2 Sheets dal gt M 4 Ready NUM 7 Fig 8 Results output with explanations in red See Tachia example files for further explanation The data can now be graphed and arranged in various tables in Excel for easy comparison It can be overlaid on a map or used for plotting or shown as trend lines throughout a phylogeny the possibilities are endless Example files Tachia 13 species TachiaRAWDATA xls Data File environmental data for 150 collections and 4 variables 2 quantitative 2 qualitative as well as collection ID numbers and geolocation data TachiaTREE nex Tree File in NEXUS format TachiaMATRIXTREE nex Tree File datamatrix and tree file in Nexus format TachiaRESULTSManualAnalysis xls Results File comments added TachiaRESULT
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