SPLATCHE: USER MANUAL - Population Genetics CMPG Lab
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1. yllcorner 36 897187 cellsize 0 83 NODATA value 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9999 9 999 99989 29999 290999 9999 9990 7 7 7 9999 9998 9989 9999 09099 9 9997 To 7 9999 9999 9999 9999 9999 7 7 7 7 7 7 9999 9999 9999 9999 9999 7 7 7 7 7 7 3 4 4 Dynamic simulations and conversion tables to obtain K and F It is possible in SPLATCH to do dynamic simulations A dynamic simulation allows variation of carrying capacity and or friction value at different time during the course of a simulation In order to set at what time the changes occur different files are needed The two main files which are set through the settings files are typically called Dynamic K txt and Dynamic F txt On the first line of each of this file appears the number of changes during a simulation Then each line one per change is composed by the time of change in generations the filename of the corresponding table see below and an arbitrary description The three components of each line must be separated by a blank space For a non dynamic simulation only the first filename is considered regardless of the number indicated on the first line Example of Dynamic_K txt file 2 0 dataSets africa veg2K txt vegetation at time 0 500 dataSets africa veg2K 500 txt doubling of vegetation at time 500 Each file name must targets to a valid corresponding table that makes the lin2. 2004 SPLATCHE a program to simulate genetic diversity taking into account environmental heterogeneity Molecular Ecology Notes 4 1 139 142 Donnelly P amp Tavar S 1995 Coalescents and genealogical structure under neutrality Annu Rev Genet 29 401 421 Ewens W J 1990 Population Genetics Theory The Past and the Future In Kluwer Academic Publishers Mathematical and Statistical developments of Evolutionary Theory 177 227 S Lessar Dordrecht Excoffier L Novembre J amp Schneider S 2000 SIMCOAL A general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography J Heredity 91 506 510 Hudson R 1990 Gene genealogies and the coalescent process 7 Oxford University Pressoxford Jin L amp Nei M 1990 Limitations of the evolutionary parsimony method of phylogenetic analysis Mol Biol Evol 7 82 102 Jukes T amp Cantor C 1969 Evolution of protein molecules In Academic press Mamalian Protein Metabolism 21 132 H N Munro New York Kimura M 1980 A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences J Mol Evol 16 111 120 Kimura M amp Weiss W H 1964 The stepping stone model of genetic structure and the decrease of genetic correlation with distance Genetics 49 561 576 Kingman J F C 1982 The coalescent Stoch Proc Appl 13 235 248 Kingma
3. 260 280 300 320 340 360 380 400 420 440 460 480 500 E Save to WMF 4 Generation Selectors allowing to change the row and the column which will select the correct deme and display the history of the number of individuals density Graph showing the history of the number of individuals density for the selected deme It is possible to zoom in and out in the graph by drawing rectangles with the mouse cursor left button down 213 SPLATCHE User Manual Second panel showing the histories of the number of emigrants in the four directions Button allowing to save the graph in Windows Metafile format 4 Genetic module 4 1 Principles Genetic simulations are always preceded by a demographic simulation Indeed a genetic simulation uses the demographic information stored in the data base generated during the demographic phase The genetic phase is based on the coalescent theory initially described by Kingman Kingman 1982 Kingman 1982 and developed in other papers Ewens 1990 Hudson 1990 Donnelly et al 1995 This theory allows the reconstruction of the genealogy of a series of sampled genes until their most recent common ancestor MRCA For neutral genes the genealogy essentially depends on the demographic factors that have influenced the history of the populations from whom the genes are drawn The implementation of the coalescent theory is a modified version of SIMCOAL Excoffier et al 2000 The principal dif
4. M number of migrants Vt JV population density population density 17 19 F occupation F occupation Build world A BUR s Show results Figure 3 1 General Setting panel The numbers correspond to a description in the text SPLATCHE User Manual 3 3 1 General Settings file name location of the settings file txt See chapter 3 4 2Error Reference source not found for the full description of a settings file Buttons allowing to open a settings file or to save a settings file Progress bar showing the remaining computation time of a current simulation The duration of a simulation in seconds is also given at the end of the computation 3 3 2 Demography related parameters Drop down menu allowing to choose among the three available demographic models Number of simulated generations The generation time is the number of time units par generation It can be set in order to get the real time while browsing the results in the Graphical outputs window Growth rate used in the demographic models This is the net growth rate used in the logistic growth phase Migration rate used in the demographic models The migration rate m is the fraction of the deme population that will migrate out at each generation For a deme population of size N the number of emigrants is then equal to N m at each generation 8 Checkbox to allow the initial density overflow If this checkbox is switched on
5. MONIE ne RP bore Sia 14 4 1 Jaiba tei a E matt annee des end A hea Aa 14 4 2 SE NES DATE Fos ce hs ya cea sane ci nn te meee 15 4 2 1 Generalin sete em aa Soe aaa hae 15 4 2 2 Mutation model specificities icici nent inraimndrinenliecte 16 4 2 3 LE Lo CON ALA SP SR ET EL 17 4 3 MUR MeS ea ineeie tala ta a a M ce 18 4 3 1 Genetic samples n eren dE Rd E E e 18 BA O tp t TIES cases siasii ne nf en AAEE EAT TEENER EES 18 4 4 1 Arlequin files ee E EE A E ata ARER 18 4 4 2 ING RUS TES Sd de 19 4 4 3 Coalescence distribution Messi eus nat en nn ade 19 4 4 4 Coalescent trees TES 25 nun batt eou tide aa a a e ee raise 19 4 4 5 MRCA TGS Rihanna tenaient aies 19 4 4 6 Other TINGS oes RE R 20 S Ackiowledgements SAS RS TC aed E a A E EN 21 6 Download Sites re sirere enina r E E a A gn dla 21 T v Referents narena ea eats a a a ET a EE A E A 21 SPLATCHE User Manual 3 Demographic and spatial expansion module 3 1 Principles The demographic and spatial expansion module allows to simulate a demographic and spatial expansion from one or many initial populations The simulation uses discrete time and space The unit of time is the generation while the unit of the 2D space is a cell also called a deme Each deme has the same size and can be considered as a homogeneous subpopulation The spatial model used in SPLATCHE is the 2D stepping stone model Kimura et al 1964 which defines a regularly spaced array of demes Each deme undergoes an indep
6. not generate the history of the whole population but only that of sampled genes and their ancestors Thus this approach is much less demanding in terms of memory and computing time That allows the simulation of complex demographic scenarios within a very broad geographical and temporal framework 4 2 Settings panel Various parameters must be defined before launching a genetic simulation The number of parameters can be seen in Figure 4 1 4 2 1 General Sample file name location of the sam file Number of simulations to be carried out Maximum of generations after which the process stop if the genealogy has not been correctly reconstructed Refresh rate generation numbers after which the display window is updated Zoom factor of the display window 15 SPLATCHE User Manual SPLATCHE lol x General Settings Demographic outputs Genetic simulations Genetic samples file dataSets_square genes_middle sam l Browse m Mutation model specificities Data type DNA 6 No of linked loci 5 Total mutation rate ay ransition fraction 0 33 9 42 No of rate categories fi Output files 14 gana Nee Gah M Coalescences simulation PF Coalescent tree simulation No of simulations 1 2 no of simulated generations 5000 Refresh rate 1 Zoom factor fe Do simulations Current time D i S D ay 156 Active demes Wi n d OWS 51 Remaining linea
7. statistics see ARLEQUIN manual Schneider et al 2000 for more details If more than one simulation is performed using one demographic simulation which is usually the case then an ARLEQUIN batch file with extension arb is also generated listing all simulated files and allowing 18 SPLATCHE User Manual one to compute statistics on the whole set of simulated files Note also that the ARLEQUIN software has a file conversion utility for exporting input data files into several other format like BIOSYS PHYLIP or GENEPOP so that files produced by SPLATCHEcould be also analyzed by these softwares after file conversion 4 4 2 Nexus files Three other types of file produced by Friction are compatible with the NEXUS file format two files with the trees extension are automatically produced and list all the simulated trees with branch lengths expressed either 7 in units of generations scaled by the population size N and therefore representing the true coalescent history of the sample of genes or ii in units of average number of substitutions per site and therefore representing the realized mutational tree These two files could be visualized with the software TREEVIEW Page 1996 For each simulation a file with paup extension could be generated This file lists all the simulated genes together with their true genealogical structure This file can be analyzed with David Swofford s PAUP software 1999 A PAUP batc
8. 2N Only one coalescent event is allowed per deme and per generation see Ray et al 2003 for a discussion about this assumption 14 SPLATCHE User Manual Migration Each gene could have arrived with an immigrant from a different deme When going back in time it means that the gene could leave the current deme with the immigrant So the probability of migration from a deme i to a deme j for a gene depends on the number of individuals that have arrived from deme j to deme i at this generation For each gene belonging to the deme i the probability of migration from deme j is equal to m N where mj is the number of immigrants from deme j to deme i during the demographic phase All the deme sizes and the numbers of immigrant between demes are taken from the database generated during the demographic simulation 2 Generation of the genetic diversity The second phase of a genetic simulation consists in generating the genetic diversity of the samples This operation is done in adding mutations independently on all branches of the genealogy assuming a uniform and constant Poisson process At the end of this process all the sampled genes have a specific genetic identity The genetic process is entirely stochastic so many genetic simulations have to be performed for each demographic simulation in order to obtain meaningful statistics We recommend at least 1 000 simulations per demographic scenario The coalescent backward approach does
9. SPLATCHE User Manual SPLATCHE USER MANUAL 1 Introduction The goal of this user manual is to describe the technical aspects of the software SPLATCHE version 1 0 This manual complements the article from Currat Ray and Excoffier published in Molecular Ecology Notes Currat et al 2004 Further details on the methodology can also be found in Ray 2003 and Currat in prep 2 Contents Introdu ti ss sien RUE NS et aaah the ieee ele eects 1 Dic CONTES SENS Se nn Ne 1 3 Demographic and spatial expansion module eee cet ceteeeeeeeesceceaeeceeceeenseeenaees 2 3 1 Principles an ne ane ne Re 2 3 2 Available demographic mod lsisisss sent a dating 2 3 3 General Settings panels sen nes nr A ei a a a 4 3 3 1 Generalin e e crass a a TE E E a 5 3 3 2 Demography related parameters ch riscadictakadnwelivdeseraadnddae mains 5 3 3 3 Environment related pardineterss cnc Sonatas wives ete tint 5 3 3 4 Qu tp t PALAIS TEES RS Re En Ne 6 3 3 5 Mait buttons et ARS A eae tee 6 34 INPUT filesinin nanan a E E a A 7 3 4 1 Initial density and origin locations ses net lee 4 3 4 2 Settings ereun pth Nt oak ea oes en Guna eh ams yee Sota de en etre 7 3 4 3 ASCII format for environmental data 8 3 4 4 Dynamic simulations and conversion tables to obtain K and F 9 3 5 Graphical outputs MINES ne M A Sot dea ea eae aes 11 3 6 Demographic outputs window 13 Ms 9 C R
10. and the size of the initial population exceeds the carrying capacity of the deme the initial population is spread over neighboring demes until all the individuals are placed in a deme The overflow function fills a deme at carrying capacity before using neighboring demes If this checkbox is switched off the size of the initial population is always the size sets in the initial density file see chapter 3 4 1 3 3 3 Environment related parameters Radio button allowing to choose how the friction values are computed When vegetation or roughness is chosen friction values are only computed from the corresponding input data set see chapter 3 4 3 If both is chosen friction values are computed by taking for each deme the mean value between the friction value from the vegetation data set and the friction value from the roughness data set SPLATCHE User Manual Button allowing to open the friction corresponding table see chapter 3 4 4 for a description of this table in the default text editor The file can then be modified and saved The world must be rebuilt after a change in this file Button allowing to open the carrying capacity corresponding table see chapter 3 4 4 for a description of this table in the default text editor The file can then be modified and saved The world must be rebuilt after a change in this file CheckBox allowing a dynamic simulation see chapter 3 4 4 The world must be rebuilt after a change in this ch
11. ate 33 fraction of substitutions being transitions for DNA Gamma A for DNA mutation variation number of Categories for DNA mutation variation Range Constrainst for microsatellite generate Arlequin file Paup files or both 0 1 2 generate migration BMP generate density BMP generate occupation BMP generate migration ASCII generate density ASCII generate occupation ASCII DP OOO OOOO 3 4 3 ASCII format for environmental data The environmental datasets that can be loaded into SPLATCH must be in ASCII raster format Two different datasets can be loaded The first one is the vegetation dataset defining to what type category of vegetation belongs each deme The second dataset is the roughness dataset defining continuous friction values such as friction computed from topography This format of the environmental dataset is composed of a header first six lines containing information on the file then a matrix of values in rows and columns The header information is as follow ncols number of columns nrows number of rows xllcorner longitude coordinate of the lower left dem yllcorner latitude coordinate of the lower left dem cellsize width of a deme cell size in same units than the coordinates NODATA value value indicating than a deme must not be considered like sea SPLATCHE User Manual Example of an environmental dataset ncols nrows xllcorner 19 845388
12. ctional part of M is not truncated Instead a multinomial distribution is used to split M emigrants to the neighboring demes see Ray 2003 This ensures that there are always M emigrants that are sent The drawback of this technique is that it requires the drawing of random numbers which increases the time required for a simulation Model 3 Stochastic migration model with absolute number of emigrants Same as Model 2 but the number of emigrants M varies stochastically as a Poisson variable centered around Nm SPLATCHE User Manual 3 3 General Settings panel The General Settings panel is the primary panel to set the demographic parameters and to launch a demographic simulation A screenshot of this panel is shown in Figure 3 1 A description of each component of this panel is given in the following sub chapters SPLATCHE 3 5 x General Settings Demographic outputs Genetic simulations Settings file settings_square txt 1 Open Settings 2 Save Settings Simulation duration sec 3 gt Demography Initial Density Overflo 8 Number of Generation Fu 5 Growth rate FL laser rate Allow density overflow J Environment Friction Dynamism Vegetation C Roughness Both Allow dynamic environments r Vizualize Tiol tables 12 Frictiol 10 T i table Outputs every 50 rail 13 M generate BMP of generate ASCII raster of
13. d to a description in the text Legend for the current display Buttons allowing to save the legend as a bitmap Radio button for the choice of color or shades of gray display 11 SPLATCHE User Manual Information on the number of active cells cells having information for the vegetation the number of rows and the number of columns Information on the density the number of rows and the number of columns when the mouse cursor is over a particular deme Number of generations for the current display Zoom for the current display Radio button to choose from displaying the density the number of emigrants or the occupation black if occupied Button allowing to save the current display as a bitmap Cursor allowing to change the current generation and the display at the chosen generation j E E ee E E Ge Buttons allowing to display the initial at generation 0 carrying capacity map the initial friction map and the proportional arrival time in each deme 12 SPLATCHE User Manual 3 6 Demographic outputs window This window allows to explore the demographic database that has been generated through a simulation SPLATCHE 10 x General Settings Demographic outputs Genetic simulations Selected deme a Selected row Selected column 8 Demographic history Migration nad 3 Number of individuals per generation Number ofindividuals 0 20 40 60 80 100 120140 160 180 200 220 240
14. eckbox 3 3 4 Output parameters Some output parameters are placed in this panel because they need to be set prior to a simulation if one wants to automatically generate these outputs during the simulation These outputs are a temporal series of graphical representations of the state of a demographic parameter number of emigrants population densities or occupation Windows Bitmaps BMP or ASCII raster can be generated The output files are placed in two folders called respectively BMP and ASCII which are created in the same folder than the setting file The filename of each output file is composed by the name of the demographic variable followed by the number of generation at which it has been created 3 Number of generations between each output files Beside the outputs for the intermediate states a series has always outputs for the initial and the final state of the simulation E 14 16 Checkboxes for the generation of BMP files 17 19 Checkboxes for the generation of ASCII raster files eo 3 5 Main buttons Button to build a world It is during a building process that memory space is allocated and that carrying capacity and friction values are computed for each D deme Button to launch a simulation If this button is grayed out it means that the world needs to be built or rebuilt e 2 Button to show the graphical output window fs SPLATCHE User Manual 3 4 Input files 3 4 1 Ini
15. endent population growth and can exchange emigrants with its four direct neighboring demes Each deme is also considered as a sub unit of the environment The environment can influence the local demography through its carrying capacity maximum number of individuals and its friction facility to migrate through These two environmental characteristics can be defined for the entire array of demes through the input of maps Variations through time of carrying capacity and or friction values are also possible 3 2 Available demographic models The logistic population growth of each deme follows a standard logistic curve of the form K N N v 1 K where K is the carrying capacity and r is the growth rate For the migration part of the demography three models are available in SPLATCH Model 1 Migration model with even number of emigrants The number of emigrants M from a deme is computed for each generation as M mN where m is the migration rate and N is the population density of the deme at generation The number of emigrants M in any of the four directions is then computed as where F is the friction of the deme in direction i north south east or west and floor means that the fractional part of the number is truncated This model always gives a total number of emigrants which is a multiple of four SPLATCHE User Manual Model 2 Migration model with absolute number of emigrants Same as Model 1 but the fra
16. erated and is a bitmap of the spatial distribution of MRCA for all the simulations joined These maps can also be visualized by means of the button Draw MRCA 15 on Figure 4 1 on the interface Similar bitmaps with the MRCAPopDensity bmp termination are generated for each sample The Time for the Most Recent Common Ancestor TMRCA for the whole tree and for each sample are also listed in a file with the tmrca extension The TMRCA are given on generation units with the bigger number corresponding to the end time of the simulation 19 SPLATCHE User Manual 4 4 6 Other files The gen file summarize statistics about the data such as the mean coalescence times the mean number of pairwise differences within and among demes and the mean length of the trees 20 SPLATCHE User Manual 5 Acknowledgements We are grateful to Stefan Schneider and Pierre Berthier for their computing assistance The development of the SPLATCHE program was possible through a Swiss NSF grant n 31 054059 98 6 Download sites SPLATCHE http cmpg unibe ch software splatche SIMCOAL http cmpg unibe ch software simcoal ARLEQUIN http cmpg unibe ch software arlequin TREEVIEW http taxonomy zoology gla ac uk rod treeview html PAUP http paup csit fsu edu 7 References Currat M in prep These D partement d Anthropologie et d Ecologie Universit de Gen ve Currat M Ray N amp Excoffier L
17. ference with SIMCOAL is that the demographic information used by genetic simulations do not come anymore from the migration matrix and historical events but from the data base generated during the demographic simulation The genetic simulation itself follows the procedure described in Excoffier et al 2000 and consists in two phases 1 Reconstruction of the genealogy The reconstruction of the genealogy is independent of the mutational process Basically a number n of genes is chosen These genes are only identified by their number and they have no genetic variability during this first phase All the n genes are associated with a geographic position in the virtual world where the demography is simulated These genes could belong to different demes in the world Then going backward in time the genealogy of these genes is reconstructed until their most recent common ancestor MRCA in the following way Going backward in time at each generation two events can occur Coalescent event if at least two genes are on the same deme they have a probability to have a common ancestor at the preceding generation a coalescent event This probability depends on the population size of the deme where the genes are located Each pair of genes has a probability 1 M of coalescence if Nj is the number of haploid individual in the deme i If there are nj genes on the deme then the probability of one coalescent event becomes n i nj 1
18. ges 55 Coalescent events 145 Migration events 5723 Status 7 z 1 Simulations Running Figure 4 1 Genetic module panel Demes where at least one gene is present appear in violet 4 2 2 Mutation model specificities For all kind of data Type of genetic data to be generated It could be DNA RFLP Microsatellite or Standard See Genetic data type Section for more details Number of fully linked loci to simulate It corresponds to the sequence length for 16 SPLATCHE User Manual DNA Mutation rate per generation for all loci taken together Specific to DNA 9 Transition bias percentage of substitutions that are transitions Gamma a amount of heterogeneity in mutation rates along the sequence according to either a discrete or continuous gamma distribution Number of categories for DNA mutation variation Specific to Microsatellite Range constraint minimum and maximum size for microsatellite 4 2 3 Genetic data Different types of molecular data could be generated RFLP DNA Microsatellites and Standard each with its own specificities RFLP data Only a pure 2 allele model is implemented Several fully linked RFLP loci can be simulated assuming a homogeneous mutational process over all loci A finite sites model is used and mutations can hit the same site several times switching the RFLP site on and off We thus assume that there is the same probability f
19. h file with extension ba is also generated 4 4 3 Coalescence distribution files A bitmap representing the spatial distribution of the coalescent events for all the simulations joined is automatically created with the TotNumCoal bmp termination This maps can also be visualized by means of the button Draw Coalescence 15 on Figure 4 1 on the interface In setting the coalescence checkbox 16 on Figure 4 1 similar bitmaps of the spatial distribution of coalescent events are generated for every simulations with the NumCoal bmp termination The times for each coalescent event and each simulation are listed on a file with coal extension Those times are given on generation units with the bigger number corresponding to the end time of the simulation 4 4 4 Coalescent trees files In settings the checkbox coalescent trees 16 on Figure 4 1 it is possible to generate for each simulation a bitmap representing the genealogical links between each node of the coalescence tree laid out spatially SPLATCHE is the first program which allows an the spatial representation of the coalescent trees Those files are terminated with CoalTree_ bmp 4 4 5 MRCA files SPLATCHE gives information on the localization and timing of the Most Recent Common Ancestor MRCA of the totality of genes sampled thus on those of the various samples A file with the termination MRCADensity bmp is automatically gen
20. k between a particular vegetation category and a carrying capacity or friction value A corresponding table is composed of a vegetation category number followed by a carrying capacity or friction value and by a description The vegetation category numbers must correspond to the numbers found in the input vegetation dataset see previous chapter SPLATCHE User Manual Example of veg2K txt file Tropical rainforest Monsoon or dry forest Tropical woodland Tropical scrub Tropical semi desert Tropical grassland Tropical extreme desert 50 Savanna Broadleaved temperate evergr Montane tropical forest Open_boreal_ woodlands Semi arid temperate woodland Tundra K z 1 2 3 4 5 6 7 8 N O1 H HA OON DN OO O GO TOO O1 Ol N O m Oo By having several corresponding tables for the carrying capacity and or the friction values it is then possible to simulate a change in the environment through time 10 SPLATCHE User Manual 3 5 Graphical outputs window Graphical Outputs Disp lay Windows Nb active cells 2500 Density Zoom 0 Nb rows 5 Row 0 nerations 204 6 ke 7 Nb columns 5 Cole lt 3 A Save to B J 10 Display Density Migratio Occupation a I 2 Legera M Color Choice eo cal 3 DRAW gt i Carr Cap Fri Arrival time i Figure 3 2 Graphical Outputs panel The numbers correspon
21. n J F C 1982 On the genealogy of large populations J Appl Proba 19A 27 43 Page R D M 1996 TREEVIEW An application to display phylogenetic trees on personal computers Comput Appl Biosci 12 357 358 3 SPLATCHE User Manual Ray N 2003 Mod lisation de la d mographie des populations humaines pr historiques l aide de donn es environnementales et g n tiques Th se Department d Anthropologie Universit de Gen ve Ray N Currat M amp Excoffier L 2003 Intra deme molecular diversity in spatially expanding populations Molecular Biology and Evolution 20 1 76 86 Schneider S Roessli D amp Excoffier L 2000 Arlequin a software for population genetics data analysis User manual ver 2 000 Geneva Genetics and Biometry Lab Dept of Anthropology University of Geneva Ey em
22. or a site loss or for a site gain Microsatellite data We have implemented a pure stepwise mutation model SMM with or without constraint on the total size of the microsatellite Several fully linked microsatellite loci can be simulated under the same mutation model constraints The output for each loci is listed as a number of repeat having started arbitrarily at 10 000 repeats The number of repeats for each gene should thus be centered around that value DNA sequence data We have implemented here several simple finite sites mutational models The user can specify the percentage of substitutions that are transitions the transition bias the amount of heterogeneity in mutation rates along a DNA sequence according to either a discrete or continuous Gamma distribution We can therefore simulate DNA sequences under a Jukes and Cantor model Jukes et al 1969 or under a Kimura 2 parameter model Kimura 1980 with or without Gamma correction for heterogeneity of mutation rates Jin et al 1990 Other mutation models that depend on the nucleotide composition of the sequence were not considered here because of their complexity and because they require specifying many additional parameters like the mutation transition matrix and the equilibrium nucleotide composition 17e SPLATCHE User Manual Standard data Following the definition given in Arlequin User Manual Schneider et al 2000 this type defines data for which the molecular basis i
23. parameters into a file and thus of being able to recover them thereafter Only the graphical parameters are not contained in the settings files An example of settings files aisre provided with SPLATCHE settings square txt with the corresponding data files in the folder called dataSets square The example file is a simple square world constituted by 50x50 demes see Ray et al 2003 The setting file is composed of 29 parameters An example corresponding to settings square txt is given below Each line starts with the value of the parameter followed by a blank a double slash and then the description of the parameter SPLATCHE User Manual dataSets square dens init txt pop source file dataSets square simplesquare asc vegetation file dataSets square simplesquare asc roughness file dataSets square Dynamic K txt Conversion table Vegetation gt K dataSets square Dynamic F txt Conversion table Vegetation gt F 3 demographic model 1 3 700 number of generations 0 10 growth rate 20 migration rate allow Initial Density overflow 0 1 static or dynamic environment 0 1 choice of friction type 0 vegetation l roughness topography 2 both dataSets square genes middle sam original genetic sample file 1 number of genetic simulations 10000 maximum number of simulated generations 0 Genetic Data Type 0 DNA 1 RFLP 2 MICROSAT 3 STANDARD 300 number of linked loci 0 001 total mutation r
24. s not particularly defined such as mere allele frequences The comparison between alleles is done at each locus For each locus the alleles could be either similar or different 4 3 Input files 4 3 1 Genetic samples A file with the extansion sam allows to specify the localization of the population sampled as well as the number of genes sampled in each population see Error Reference source not found On the first line of this file the user can specify the number integer of population sampled The second line is reserved for the legends Then each line defines a sample with 4 fields separated by tab our space character 1 Name of the population from which the sample has been drawn 2 Number of genes belonging to that sample 3 amp 4 Geographic location of the population latitude and longitude SPLATCHE will determine automatically in which particular deme falls the coordinates of the population The coordinates must belong to the geographical surface defined in the header file c Example of a genetic input file sam for 6 samples in Africa 4 4 Output files on Figure 4 1 Various kinds of genetic output files can be generated by SPLATCHE 4 4 1 Arlequin files The genetic data generated by one simulation are directly output in an ARLEQUIN project file with the extension arp This file format allowing one to compute the data using the ARLEQUIN software in order to obtain different
25. tial density and origin location A file called dens_init txt in the examples is used to specify the place of origin of the simulated population This file contains a first line of legend and a second line defining the population source This second line consists of 5 fields separated by tab or space character 1 Name of the source population 2 Size of the source population in number of effective haploid individuals 3 amp 4 Geographic coordinates of the population source latitude and longitude SPLATCHE will determine itself in which particular deme corresponds the coordinates of the population Coordinates must belong to the geographical surface defined in the header of the environmental files Coordinates do not need to be in a particular units e g decimal degrees but they needs to be in the same units that the coordinates defined in the header of the environmental files 5 Resize parameter it is the size of the population source before the beginning of the expansion This parameter is used only for genetic simulations If this parameter is set to 0 then the size of the population source before the onset of the expansion is regarded as being equal to the initial size parameter 2 Example of initial density file Name Size Lat Long Resize middle 100 1 LS 0 3 4 2 Settings file All the parameters can be defined using the graphical interface of SPLATCHE However it is possible to save a group of
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