cdpop user manual - Computational Ecology Laboratory
Contents
1. Y CDClimate N then a new cost distance matrix will be read in at a specified generation time in next column CDclimgen The generation time that the new cost distance 10 time matrix will be read in at A NxN future cost distance matrix for mating movement where N gt n and n is the number of Futuremate EDcdmatrixl6 grid values or individuals on the landscape cdmat i This is a comma delimited file format Note that this file must be the same size as the initial cost distance matrices used in the simulations A NxN future cost distance matrix for dispersal movement where N gt n and n is the number of grid Futuredisp EDcdmatrixl6 values or individuals on the landscape This cdmat i is a comma delimited file format Note that this file must be the same size as the initial cost distance matrices used in the simulations 4 Output The following is a list o F options to calculate cost matrix genetic distance matrices output options from CDPOP including distance matrices Euclidean distance and genotype formatting File Header Example Description MateCDmatans This is the mating cost distance matrix answer If Y then the cost distance matrix used for the n grid locations is extracted from the N mating cost distance matrix locations If N entered this matrix is not created Note that currently only the initial cost distance matrix is used to create this matrix not2. Section 3 contains a breakdown parameters that can be changed The Input the file You will need to CHANGE the Directory column s information to your home directory as noted in Step 1 For example I would change text in A2 and A3 using Excel to point to my home directory for this example run to read C CDPOP ExampleRun BE SURE to remember to put the final forward slash at the end of the path name save a comma delimited Excel questions about saving in this After you hav inpu fil form made the home directory change in step 3 tvariables in the same format inputvariables csv Select Yes or OK for any at Start the program with a graphical interface or at the command line example if you downloaded Python 2 6 x from www python org provided with a graphical interface IDLE In Windows you can find IDLE from your Start menu gt All Programs gt Python 2 6 gt IDLE Python GUI Alternatively if you use python from the command line then open a terminal window and change your shell directory to the CDPOP home directory For then you are Run the program There are a number of ways to run open CDPOP py by going to File gt Open directory clicking on CDPOP py and OK A new window will appear with CDPOP py source code In the menu bar click Run gt Run Module If you are using a command shell you can run the program by typing python CDPOP py IDL En
3. used to initialize the model s n individual s genotype If N is entered then this file is not used If you want to use a frequency distribution file you must set intgenesans to equal file and then enter in the filename in this field S allelefrequency csv example file for formatting this file Alleles 10 The number of alleles per locus mtDNA If Y then last locus becomes mtDNA and every offspring inherits this locus from its mother only If N then regular Mendal inheritance occurs 3 7 CDEVOLVE The following lists the parameters and selection surfaces used to Simulate nat ural selectio N File Header Example Description CDPOP user manual 13 Cdevolve This is the selection answer SY Ors ANY response to turn on CDEVOLVE natural selection Alleles must be 2 if Y is entered AdultMortFit Fitvals100 t xt This is the adult viability selection surface If adult has AA or Aa then this mortality fitness surface is used which increases the individuals chance of survival if oldmortperc gt this fitness surface value Oldmortperc is used for individuals that have aa To turn this selection function off when cdevolve Y then set oldmortperc this fitness surface Offspring MortFitAA Fitvals0 txt This is the offspring viability selection surface for AA If offspring
4. 2010b Cushman and Landguth 2010 Example sim ulations have included e Quantifying the time to detect barriers e Correlate migration rates and landscape resistance barriers e Testing for the effects of population sample size and number of markers CDPOP user manual 4 1 3 How does CDPOP work CDPOP v1 0 models genetic exchange for a given resistance surface and n x y located individuals as functions of individual based movement through mating and dispersal vital dynamics and mutation A user must specify the input parameters through a graphical user interface or input script file As the model simulates stochastic processes most applications will quantify mean and variability of genetic structure across many runs Thus a Monte Carlo option is provided for the user to choose the number of runs to simulate given a single set of input parameters In addition a user may also frequently wish to launch several runs with different parameter values Simultaneously i e sensitivity analysis This functionality is provided through batch capability The simulation program assumes constant population density over time Individuals are assumed to occupy a fixed grid on the landscape that is user defined by the n x y located individuals The genotype of each locus for each individual can be initialized by randomly choosing from a file containing allele frequencies
5. genetic distance matrices This value is used if nthfile choice Sequence This is the by value in the sequence For example 1 would create values starting at 0 ending at looptime 1 by every 1 generation Panans Use this parameter to specify whether or not there is panmixia in your populations For example your resistance surface may include a barrier that separates populations that include panmixia on either side This allows you to include random movement with landscape effects Possible values to enter are N and Y Twopopans Use this parameter with panans Y to test two populations that are separated by a landscape feature and follow random movement within their respective populations This is for a specific set of simulations that assumes only two populations in your study Possible values to enter are N and Y Oldmortperc 100 Percent mortality in the adult population 3 3 The following Mating pa lists the parameters used for the movement of rameters individuals due to mating File Header Example Description Movement function answer for mating 1 Linear 2 Matemoveno 1 Inverse Square 3 Nearest Neighbor 4 Random Mixing 5 Negative Exponential This is only used for negativ xponential MatemoveparA 1 Y g p Y a 10 bx and is the parameter a CDPOP user manual 11 MatemoveparB This is only used for
6. has AA then this mortality fitness surface is used which increases the individuals chance of survival if newmortperc gt this fitness surface value Newmortperc is used for offspring that have Aa or aa To turn this selection function off when cdevolve Y then set newmortperc this fitness surface mortality value Offspring MortFitAa Fitvals0 txt This is the offspring viability selection surface for Aa If offspring has Aa then this mortality fitness surface is used which increases the individuals chance of survival if newmortperc gt this fitness surface value Newmortperc is used for offspring that have AA or aa To turn this selection function off when cdevolve Y then set newmortperc this fitness surface mortality value Offspring MortFitaa Fitvals0 txt This is the offspring viability selection surface for aa If offspring has aa then this mortality fitness surface is used which increases the individual s chance of survival if newmortperc gt this fitness surface value Newmortperc is used for offspring that have AA or Aa To turn this selection function off when cdevolve Y then set newmortperc this fitness surface mortality value Fecundity Fitvalsl txt This is the fecundity selection surface Fecundity surface is proportion of offspring for aa Use with constant offspring at set level e g of no 3 and lambda 10 would produce 10 offspr
7. ll see the version number on the top line enter Control D to exit Replacing an older Python interpreter pre v2 4 with a newer one v 2 6 x on a Linux or MAC OS X machine can be tricky so ask a System Administrator for help if you re not sure which packages depend on the current Python installed 2 1 3 Python on Windows Windows 7 XP 2000 Server does not come with Python installed so follow the instructions below to obtain and install Python ona computer running the Windows operating system Get a windows installation of the base Python installation current v 2 6 x at http www python org download releases 2 1 4 Obtaining NumPy and SciPy We recommend using the superpack Windows installer available from the SourceForge website http sourceforge net project Note that more complete information for NumPy is available at www scipy org where the SciPy module is also presented Another source is http www enthought com products epd php for a free academic and educational usage in a single downloadable installer that has everything and then some Numpy Scipy Matplotlib and 70 modules for python 2 2 Installation 2 2 1 Install Python NumPy and SciPy Make sure that Python and NumPy are installed and available to you You can test this by typing python at a command window If python is available you ll get the python prompt gt gt gt If it is not a recognized
8. this program In then browsing to your home Check for successful model run comple by step output in the Shell window will be printed out and folders batch batchrunimcrunl will be created in yo output from the separate batch and or folders will have a unique date time case you want to run multiple CDPOP r tion Once completed runOmcrun0O ur CDPOP home direc Monte Carlo runs stamp preceding ba uns in this same di as The program will provide s batchrunlmcrunO tep imulation time and tory to store Each of these tchrunOmcrunO in rectory The CDPOP user manual 9 program will also provide a log file with program steps in your CDPOP home directory 2 3 2GUI Run The following are instructions for a simulation run with an optional graphical us r interfac on python library GUI WX python Note that this GUI has a dependency Go to http wxpython org download php and download your OS s version of WX python 1 Navigate to CDPOP folder and double click cdpopi py 2 Enter in values for each variable a specific variable variable label 3 After all values ar ntered To find out more information on click the radio button to the right of the click the Submit button at the bottom If a bottom value is in the wrong format f you will be notified at the 4 The program is r
9. 0 Lmbd 5 lmbda to draw randomly from If offno 2 then S lmbda is the Poisson mean for the litter siz If offno 3 then lmbda is the constant litter size value Female 50 Percent number of female born in each litter percent ot The answer to have every generation start with Equalsex i mae Y equal sex ratios Possible options include N ratio and Y newmortperc 0 Percent mortality in the offspring population 3 6 Genetic parameters The following lists the parameters associated with the initialization of the genotypes mutatio n rates and mtDNA option File Header Example Description Geneswapgen 0 The generation time that genetic information is exchanged Muterate 0 0005 The k allele model mutation rate Loci 10 The number of loci Intgenesans random The choice for how to initialize the genotype for each n x y individuals If random is ntered then the genotypes get a random assignment and the population is at a maximum genetic diversity If file is entered then the genetics get drawn from the allele frequency distribution file specified in next column allefregfilename If known is entered then the genotypes are directly read from a given known file Email Erin Landguth for an example file to use for Known Allefreg filename The allele frequency distribution for each locus
10. A A 9 3 1 TAPUE Fi VES A A IAE e 9 32 Model ParametertSsy iii at ad 10 33 3 Mating Parameters A A AA aS 10 3 4 Dispersal Parameters sae sc Sait we eh ae a bee dy dadas 11 325 OLPSPYING Parameters eere ee a a ad ieee es 11 350 Genetica Parameters ai ia dao as a a 12 3301 CDE MO TIN Bittle ecie o ve eee Seid eco ale A ws hse ere Rte Se A A teen E 12 3 8 COINTE T i e rad OO eee ESR ya de 13 3 69 EDELAMATE as A tae che cata A able arte wane eee Si ies whoa ance ee 14 An OUTED a sal sc sas aa Sec Rae Parr Boe a Se gh Rae ita BE ee et Cee aS 14 5 General DVSSUSS iba pa bee deel GR ane al aS al BN ore erg Sai chs Sue eee ee wes 15 Salo How to Obtawn CDPOB acra aea e E E T a Be e E SEB ae 15 52 Debugging and troubleshootinG oooooooooooooo ooo 15 53 gt HOW tO eTte CDPOP as vtec tie ae e a A id E E AA e 15 REFETENCES iy eoma nhai pe a a A ee ws i eG a 16 dy AEKNOWLEAGOMEN ES ses meaa a aa SA tada jo a a ee wa di 17 CDPOP user manual 3 1 Introduction The goal of this user manual is to explain the technical aspects of the current release of the CDPOP program CDPOP v1 0 is a major extension of the CDPOP program Landguth and Cushman 2010 CDPOP is an individual based program that simulates the influences of landscape structure on emergence of spatial patterns in population genetic data as functions of individual based movement breeding and dispersal 1 1 Changes from CDPOP v0 7 Ther
11. CDPOP user manual 1 CDPOP USER MANUAL 2011 Version 1 0 Authors E L Landguth B K Hand J M Glassy S A Cushman and M Jacobi 1 University of Montana Division of Biological Sciences Missoula MT 59812 USA 2 Lupine Logic Inc Missoula MT 59802 USA 3 U S Forest Service Rocky Mountain Research Station 2500 S Pine Knoll Dr Flagstaff AZ 86001 USA CDPOP user manual 2 Table of Contents gt AMECLOQUELLON hi A AA A AO AE AS ered ers 3 Ll Changes trom CDPOP VU a nia eee 3 t27 What Can CDLOP do laa sd a a ares 3 123 How does lt CDPOP WORK siii A A AA 3 2 GEREING Started sis is A A AA A pee a 5 2rd DE PENGENCLES ik 4 ernes A E E E E EEE ee eS 5 2 1 1 Baseline requirementS o oooooooooooooooooooo 5 2 122 Python On NON WIMdOws platos sisi delas a et 6 2453 PYTHON On WINAOWS se sate li a 6 2 c4 0btai nang NumPy and SELL Y 2 AA os 6 22 ETS ba l ration a oi ceed ie foe tt be at ata A Bey A ohh dada IAM ta tadas 6 2 21 Installing Python NumPy and SCLPY eii odds 6 22262 Unpack the iCDPOP archiveros Mie den Sled See deus 7 2 2 3 Insta SD POD nie coe Dr e Da 7 Za DESCripELON O F iCDPOR Lleida aras cal 7 QoS EXAMPLE eile te da A A we a da ae TR 7 2 Se 1eCommand LUNAS Fun ale k at as 8 LS oll GUT UA A ER ae Na A o 9 a
12. ack the supplied zip archive file using a free archive tool like 7Zip 7z exe Pkunzip Unzip or an equivalent Seven Zip 7Z exe is highly recommended since it can handle all common formats on Windows MAC OS X and Linux On Windows it is best to setup a project specific modeling subdirectory to perform your modeling outside of any folder that has spaces in its name like My Documents 2 2 3 Install CDPOP Next install the CDPOP software itself by unpacking the zip archive supplied At this point you should be able to execute the supplied test inputs 2 2 4 Description of CDPOP files 20 files will be installed in your directory Here is a description of each EADME txt a quick how to run CDPOP instructions DTablel6 csv example N x y for the cost distance matrix o HG a W Dcdmatrixl6 csv example Euclidean distance cost distance matrix ED16 csv example n x y for individuals P POP py Python driver code and run file POP Disperse py Python library for the dispersal functions POP GetMetrics py Python library for the metric functions POP Mate py Python library of the mating functions POP Modules py Python library with general functions POP Offspring py Python library for the offspring functions O Y OD 0 RD POP PostProcess py Python post processing library Oo 00000000 DPOP PreProcess py Python pre processing library e cdpopi py GUI python file t
13. ange of climate surface at a given To address this need CDPOP generation time through new cost distance matrices for both mating and dispersal The program is written in Python 2 6 and provided with installation along with plug in instructions for most platforms v1 0 is built on a driver module E allows for ease of future modular development debugged as carefully as possible by testin simulation options Information for users sample input files CDPOP docking architecture that g all inc FAQ publications ongoing research developer involvement downloads can be found at http cel dbs um 2 Getting started 2 1 Dependencies and CDPOP v1 0 has been combinations of uding user manual t edu software CDPOP CDPOP user manual 6 2 1 1 Baseline Requirements CDPOP requires the Python2 6 x interpreter NumPy package and SciPy package Remember that Python modules usually require particular Python interpreters so be sure the version ID for any external Python module or package e g NumPy or others matches the version of your Python interpreter normally v2 6 x 2 1 2 Python on Non Windows Platforms Some common computer platforms come with Python installed These include MAC OS X and most Linux distributions To determine which Python a MAC or Linux workstation has installed start a terminal console and enter python You
14. atrix filename EDcdmatrixl6 A NxN cost distance matrix for dispersal movement where N gt n and n is the number of grid values or individuals on the landscape CDPOP user manual 10 This is a comma delimited fil Xycdmatrix filename CDTablel6 The N x y coordinate values for both the mating and dispersal cost distance matrices This is a comma delimited file with a header row X Y 3 2 The following Model parameters list are the model parameters used for CDPOP File Header Example Description Mcruns 1 The repeated number of simulations to be conducted for the Monte Carlo method Looptime Simulation run time generation File output indexed from 0 looptime 1 Nthfile choice Sequence The choice of a specified simulation run time to write to file and to calculate genetic distance matrices If List is entered then read nthfile list values below If Sequence is ntered then read nthfile seq value below Nthfile List 01314 The specified simulation run time to write to file and to calculate genetic distance matrices These values are used if nthfile choice List These values must be separated with a vertical bar Note that maximum value in Nthfile List must be Looptime 1 due to indexing starting at 0 Nthfile Seq The specified simulation run time to write to file and to calculate
15. command it means either that python is installed but is not in your command shell s paths or that python is not installed In the first case ask an administrator to add it to your command paths If your shell locates and loads python type import numpy Similarly type import scipy If python does not complain that there are no such modules all is well The following instructions assume Python NumPy and SciPy are not yet available on your computer if they are skip to section 2 2 2 First run the Python executable installer you ve chosen either from www python org or ActiveState accepting defaults for the installation CDPOP user manual 7 directory On Windows this will typically place the executables and libraries in c Python2 6 bin and the site packages package tree for user installed Python modules in c Python2 6 lib site packages If you are installing it on a network on which you do not have administrative privileges you may need to ask a system administrator to install python and the NumPy and SciPy packages in their default locations Next install NumPy and SciPy using the supplied executable superpack installer or visiting http www scipy org Download This will install NumPy and SciPy in your Python site packages directory 2 2 2 Unpack the CDPOP Archive Navigate to the directory on your PC where you wish to install CDPOP and unp
16. e are major innovations in v1 0 which were not included in the previously published v0 70 We list below the new functionalities of CDPOP v1 0 e Natural selection is implemented through differential offspring viability as functions of fitness landscapes e Gene flow and natural selection can now be simulated in dynamic landscapes e A graphical user interface provides a user friendly platform that enables users to explore analyze and model the effects of life history and differential models of complex landscapes on the genetic structure of populations F e Sex speci e Module driver plug in architecture ic dispersal F e Changes of some internal software components have allowed an overall speed increase and to improve program stability e Additional movement function option negative exponential movement e Inclusion of both a mating landscape and a dispersal landscape e Vertical transmission of an infection e mtDNA option e Output genotype option in a general genetic format 1 2 What can CDPOP do CDPOP s realistic representation of the spatial environment and popu lation genetic processes provide a powerful framework to investigate the impact of ecological factors on the genetic structure of popula tions This approach has already advanced knowledge of the patterns of genetic variation in spatially explicit contexts Landguth et al 2010a Landguth et al
17. eeware and can be downloaded at http cel dbs umt edu software CDPOP with information for users including manual instructions FAQ and developer involvement 5 2 Debugging and troubleshooting publications ongoing research For help with installation problems please check first for postings at our web site Otherwise pleas me at erin landguth mso umt edu 5 3 How to cite CDPOP report problems including any bugs to This program was developed by Erin Landguth with help from Brian Hand Joe Glassy and Sam Cushman GUI The reference to cite is Landguth EL Hand BK Glassy UM development was done by Mike Jacobi Cushman SA Jacobi M 2011 CDPOP v1 0 An individual based landscape genetics program Bioinformatics Submitted 5 4 Disclaimer The software is in the public domain and the recipient may not assert any proprietary rights thereto nor represent it to anyone as other than a University of Montana produced program version 1 x CDPOP is provided as is without warranty of any kind including but not limited to the implied warranties of merchantability and fitness for a particular purpose The user assumes all responsibility for the accuracy and suitability of this program for a specific application In no event will the authors or the University be liable for any damages including lost profits lost savings or other incidental
18. for each locus or by reading in a file containing the initial multi locus genotypes of all the individuals The initial age structure of the population is specified by an input file specifying initial age frequency The sex of each initial individual is randomly assigned There are five movement functions that define how individuals choose a mate and disperse on the landscape as a function of cost distance linear inverse square negative exponential nearest neighbor and random mixing With the nearest neighbor movement function an individual moves to the available grid location nearest its initial location Random mixing moves an individual to a grid location that is randomly chosen from the n grids in the population In linear inverse square and negative exponential movement functions individuals move a distance from their initial location based on a draw from a probability distribution inversely proportional to a linear inverse square or negative exponential function The user specifies the maximum dispersal distance in cost units an individual can travel on the landscape The probability is one at no distance from the original location and goes to zero at the maximum dispersal distance Reproduction is defined by the user as either hermaphroditic or heterosexual With hermaphroditic mating there are no distinct sexes but individuals mate wit
19. g samples Molecular Ecology Notes 5 177 180 Storfer A et al 2010 Landscape genetics where are we now Molecular Ecology 19 3496 3514 CDPOP user manual 17 Wright S 1932 The roles of mutation inbreeding crossbreeding and selection in evolution Proceedings XI International Congress of Genetics 1 356 366 7 Acknowledgements This research was supported in part by funds provided by the Rocky Mountain Research Station Forest Service U S Department of Agriculture and by the National Science Foundation grant DGE 0504628
20. h other individuals according to the movement function choice exchanging genes in Mendelian reproduction In heterosexual reproduction mated pairs are one male to possibly many or no females and the end of the mating process occurs when all females have mated Each mated pair can have a number of offspring that is a bounded random draw based on a uniform probability distribution a Poisson draw with specified mean or a constant number Mendelian inheritance with k allele mutation rate chosen by the user is used to generate the offspring s genotype and the sex assignment is random Dispersal of offspring occurs from according to the selected movement individual The vital rates birth the population will have emigrants and deat Simulating natural selection sources of genetic variation gene flow ge These versions assumed that different genot probability of surviving and passing on the generations and thus natural selection was 1 0 implements natural selection analogousl fitness landscape of all frequencies functionality enables y investigate the links between ge Wright CDPOP user manual 5 the mother s x y location function and the sex of the whether or not defin h or immigrants netic drift ypes have an equal ir alleles to future not operating y to the adaptive or 1932 ne flow an explicitl complex landscapes at an
21. individual s level 3 locus th is under selection For example ndscape surfaces for each genotype o The user specifies This new xtension of landscape genetic analyses to d selection in Past versions of CDPOP modeled three and mutation CDPOP V lelic f a single dial three relative f fitness 1 at surfaces must be specified f two alleles A and a for the three ge Selection i notypes AA Aa s implemen from the differential survival Po relative individual location pre processing step settles the same as CDPOP with an additional step implement sel the dispersal process Simulating dynamic landscapes The potential impacts of climate change on the connectivity of populations have become an area of concern among scientists and land managers quantitative and spatially explicit predict specific fitness values for each n The program will continue all other processes ection during otype and x y individual itness and aa ted through of dispersing individuals as a function of the fitness at the location on that surface where the dispersing CDPOP v1 0 reads and extracts gen in the Current needs incl ions of current and potential future patterns of fragmentation change scenarios Opdam Wascher 2003 v1 0 allows users to input a new landscape ude under a r
22. ing for every mother with AA and Aa Then the Fecundity selection is performed for individuals with aa and fitness surface at proportion of set offspring level eg 0 10 would produce 1 offspring for every mother with aa 3 8 vertical tra CDINFECT These parameters are used with the module CD is assumed nsmission horizontal NFECT Currently only Future development will include transmission parameters File Header Example Description This is the infection parameter answer This CDInfect N tracks vertical transmission in the population If Y then a random status infection 0 or 1 CDPOP user manual 14 is created and initialized for each individual If N then the status 0 is created for all individuals and initialized A column in grid csv denotes the infection status at each generation for every individual This is the transmission probability for if a T j j aces e 0 5 parent has the infection the chance that the P infection will be passed along to the offspring 3 9 CDCLIMATE These are the parameters that control the dynamic landscape functionality within CDPOP cost distance matrices ar A generation time is specified and input then read into the program and used in Simulations File Header Example Description This is the dynamic landscape answer If
23. ion of human evolutionary trees with polymorphic micorsatellites Nature 368 455 457 Cushman S A et al 2006 Gene Flow in Complex Landscapes Testing Multiple Hypotheses with Casual Modeling The American Naturalist 168 486 499 Cushman S A and Landguth E L 2010 Spurious correlations and inferences in landscape genetics Molecular Ecology 19 3592 3602 Holderegger R and Wagner H H 2006 A brief guide to Landscape Genetics Landscape Ecology 21 793 796 Landguth E L and Cushman S A 2010 CDPOP A spatially explicit cost distance population genetics program Molecular Ecology Resources 10 156 161 Landguth E L et al 2010a Quantifying the lag time to detect barriers in landscape genetics Molecular Ecology 19 4179 4191 Landguth E L et al 2010b Relationships between migration rates and landscape resistance assessed using individual based simulations Molecular Ecology Resources 10 854 862 Legendre P and Legendre L 1998 Numerical ecology 2 English ed Elsevier Amsterdam McRae B H and Beier P 2007 Circuit theory predicts gene flow in plant and animal populations Proceedings of the National Academy of Science USA 104 19885 19890 Nei M et al 1983 Accuracy of estimated phylogenetic trees from molecular data Journal of Molecular Evolution 19 153 170 Ray N 2005 PATHMATRIX a GIS tool to compute effective distances amon
24. negativ a 10 bx and is the parameter b xponential y Matemove thresh A threshold option in cost distance units for how far an individual can search for a mate You can specify max to consider all individuals for mating movement You can also place a integer value in front of max to consider a percent cost distance movement for mating For example 10max would consider all mating individuals that are within 10 percent of the maximum cost distance on the surface Freplace If you want females to mate with replacement then specify Y If you want females to mate without replacement then specify N Mreplace If you want males to mate with replacement then specify Y If you want males to mate without replacement then specify N Selfans If you want to allowing selfing i e individuals mate with themselves then specify Y If you do not want to allow for selfing then specify N Sexans Y for sexual reproduction and N for asexual reproduction Reproage The age at which individuals can reproduce Use with overlapping generations i e oldmortperc not set to 100 3 4 Dispersal parameters Here lists the parameters used for the movement of individuals with regards to offspring dispersal File Header Example Description This is the func
25. o run CDPOP py e agedistribution csv xample age distribution file e allelefrequency csv xample allele frequency distribution file e fitvals0 txt xample fitness landscape for offspring selection e fitvalsl txt xample fitness landscape for fecundity selection e fitvals100 txt xample fitness landscape for adult selection e inputvariables csv run parameters corresponding to th xample files e RipMgr py installation file for package RipMgr CDPOP user manual 8 2 3 Example run 2 3 1 Command line run The example run is for 16 points representing individual Euclidean distance cost distance matrix follow these steps s with a To run the following example Double check that the twenty files provided in the archive are in the same directory Make a note of this directory name which we will call the home directory for example I would save all of the archive information in a location named C CDPOP ExampleRun The included file inputvaribles csv specifies the parameters that can be changed and used in a sample CDPOP run Open inputvaribles csv in your editor of choice A spreadsheet program like Microsoft Excel allows for easy editing of the tabular values a header line to 2 separate CDPOP runs batch for each column header and the listed is for the first row in There will be 3 lines of information in inputvariables csv and 2 lines of information corresponding process
26. or consequential damages arising from the use of or the inability to use this program CDPOP user manual 16 We strongly urge you to read the entire documentation before ever run ning CDPOP We wish to remind users that we are not in the commercial software marketing business We are scientists who recognized the need for a tool like CDPOP to assist us in our research on landscape ecology issues Therefore we do not wish to spend a great deal of time consulting on trivial matters concerning the use of CDPOP How ever we do recognize an obligation to provide some level of infor mation support Of course we welcome and encourage your criticisms and suggestions about the program at all times We will welcome ques tions about how to run CDPOP or interpret the output only after you have read the entire documentation This is only fair and will elimi nate many trivial questions Finally we are always interested in learning about how others have applied CDPOP in ecological investiga tion and management application Therefore w ncourage you to con tact us and describe your application after using CDPOP F We hope that CDPOP is of great assistance in your work and we look forward to hearing about your applications 6 References Allendorf F W and Luikart G 2007 Conservation and the genetics of populations Blackwell Malden MA Bowcock A M et al 1994 High resolut
27. the futurematecdmat is DispCDmatans This is the dispersal cost distance matrix answer If Y then the cost distance matrix used for the n grid locations is extracted from the N dispersal cost distance locations If N is entered then this matrix is not created Note that only the initial cost distance matrix is used to create this dispersal cost distance matrix not the futuredispcdmat CDPOP user manual 15 Edmatans N This is the Y then the Euclidean distance matrix answer If Euclidean distance matrix used for the n grid locations is calculated It N is entered then this matrix is not created Gendmatans Dps This is the genetic distance matrix answer The genetic dis locations for specified generation time of the simulation run is calculated Enter braycurtis for the Bray Curtis distance measure Dps for the proportion of shared alleles or Da for Nei s genetic distance Note that Nei s genetic distanc tance matrix used for the n grid takes the longest to calculate and may decrease your total CDPOP simulation time Gridformat General This is the genotype output format option The format for the genotype output is specified by entering general for a general genotype output or for the cdpop genotype output 5 General issues 5 1 How to obtain CDPOP The program is fr
28. tion answer for female movement for SR 2 dispersal 1 Linear 2 Inverse Square 3 Nearest Neighbor 4 Random Mixing 5 Negative Exponetial Fdispmove 1 Used only for negativ xponential y a 10 bx and parA is the parameter a Fdispmove 1 Used only for negativ xponential y a 10 bx and parB is the parameter b A threshold option in cost distance units for how Fdispmove Pies i f ehrest 5 far an individual female offspring can disperse on the landscape This is the function answer for male movement for Mdispmoveno 1 dispersal 1 Linear 2 Inverse Square 3 Nearest Neighbor 4 Random Mixing 5 Negative Exponential Mdispmove 1 Used only for negativ xponential y a 10 bx and parA is the parameter a Mdispmove 1 Used only for negativ xponential y a 10 bx and parB is the parameter b Mdispmove 10 A threshold option in cost distance units for how thresh far an individual male offspring can disperse 3 5 Offspring parameters The following list are the parameters to deal with offspring births and deaths CDPOP user manual 12 File Header Example Description This is the litter size or the number of Offno 2 offspring each mate pair can have Choose 1 for a random draw 2 for Poisson draw and 3 for a constant number of offspring for each mother The parameter value used with offno If offno 1 then lmbda is the max range value between
29. unning successfully if the command prompt opens up and displays text related to running CDPOP and output folders created in your directory 3 Input 3 1 Input files The following are the general provided for formatting input files used in CDPOP See examples File Header Example Description Directory CHANGE Home directory location of all CDPOP files Change this to match the pathname of the location of all CDPOP files Make sure to include the final forward slash at the end of the pathname Xyfilename xyED16 The n x y grid location values This is a comma delimited file with 5 column headings a unique identifier FID x coordinate location XCOORD y coordinate location YCOORD a string label identifier ID and an initial sex assignment sex See xyED16 csv for an example xyfilename agefilename The distribution that is used to initialize the model s n individuals age structure If N is entered then this file is not used If a filename is entered then read in the file for example agedistribution would be entered for the example provided See the agedistribution csv for formatting this file Matecdmatrix filename EDcdmatrixl6 A NxN cost distance matrix for mating movement where N gt n and n is the number of grid values or individuals on the landscape This is a comma delimited fil Dispcdm
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