CDPOP user manual - Computational Ecology Laboratory
Contents
1. Dispersal square movement for female dispersal Movement probability probability Choice function for female cost See Mating Movement Choice distance movement Female Fdispmovepar 1 This is the A parameter used Dispersal A for the function in movement ovement answer bt E Parameter Female Fdispmovepar 1 This is the B parameter used Dispersal B for the function in movement ovement answer 5 V Parameter Female Fdispmovepar 1 This is the C parameter used Dispersal e for the function in movement ovement answer 7 Parameter Female Fdispmovethr 75max will A threshold option in cost Dispersal esh move 75 of the distance units for how far an ovement maximum cost individual female offspring can Threshold distance on that disperse You can specify max surface to consider all individuals for mating movement You can also place an 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 You can also just specify a specific cost distance value ale Mdispmoveno 2 inverse This is the function answer for Dispersal square probability movement for male dispersal ovement function for male Choice co2. Future Futuredispcd EDcdmatrix16 A nxn future cost distance CDPOP user manual 28 Dispersal CD Matrix mat EDcdmatrixl6 matrix for dispersal movement where n is the number of grid values or individuals on the landscape 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 If you are using multiple surfaces i e you specified multiple cdclimate generations by separating them with then you will also need to specify multiple cost distance matrices here as well by using a ED Matrix Edmatans N a Euclidean distance matrix is not calculated This is the Euclidean distance matrix answer This matrix will be called EDmatrix csv and output in the respective batch and Monte Carlo folder If Y then the Euclidean distance matrix used for the n original grid locations is calculated If N is entered then this matrix is not created GD Matrix Gendmatans Dps proportion of shared alleles genetic distance matrix is produced for every grid csv file This is the genetic distance matrix answer The genetic distance matrix used for the n original grid locations for specified generation time of the simulation run is c
3. 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 Y 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 among samples Molecular Ecology Notes 5 177 180 1 Storfer A et al 2010 Landscape genetics where are we now Molecular Ecology 19 3496 3514 Wright S 1932 The roles of mutation inbreeding crossbreeding and selection in evolution Proceedings XI International Congress of Genetics 1 356 366 10 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
4. CDPOP user manual 7 2 Getting started 2 1 Dependencies 2 1 2 Baseline Requirements CDPOP requires the Python2 7 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 7 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 1ll 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 7 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 7 x at http www python org download releases 2 1 4 Obtaining NumPy and SciPy A good suggestion for all in one installations is through the superpack Wind
5. turned o TE selfing is FF 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 Reproduction Answer sexans SNE sexual reproduction is choosen Y for sexual reproduction In sexual reproduction mated pairs consider male and females with or without replacement N for asexual With asexual reproduction n individuals mate and bear offspring with mates selected according to the movement function choice and without regard to any gender or mating type It is important to note that this asexual reproduction is functionally the sexual paring of hermaphroditic individuals thus it is asexual in the sense that there are no distinct sexes but is sexual in the sense that individuals mate with other individuals exchanging genes in Mendelian reproduction reproduction all Reproduction Age reproage VQ individuals start reproducing at age 0 The age at which individuals can start to reproduce Use with overlapping generations i e agemortperc not set to 100 If an age distribution file is not used then age gets initialized with 0 at the starting generation Female Fdispmoveno vo inverse This is the function answer for CDPOP user manual 18
6. This will ensure that each litter is equal sex ratio but not necessary ensure that the generation will result in equal sex ratio after dispersal do to unbiased dispersal parameters and stochastic dispersal i e random offspring chosen for dispersal N This option is not used and offspring sex is assigned using the Female percent parameter above Birth ortality birthmortper C vo 0 birth mortality Percent mortality in the offspring population Age Structure ortality agemortperc 1100 Age structured mortality here with non overlapping generations This is the mortality field for each age class Each age class must be separated with a If looking at no generations the numbers offspri n overlapping n specify ng mortality which is the same as the birth mortality in this situation and adult mortality where adult mortality is set to 100 generations with distribution class classes 0 1 2 If looking at overlapping a supplied age e g age 3 4 then a mortality percentage must be CDPOP user manual 22 entered for each age class e g 50 20 20 30 100 Note that if you do not put 100 for the final age class then the population will be allowed to go beyond your last age class specified All age classes beyond specified in file will get lumped into la
7. Command line run The example run is for 16 points representing individuals with a cost distance matrix calculated with Euclidean distance To run the following example follow these steps 1 Double check that the 3 directories provided in the archive are in the same directory 2 The included file inputvariblesl pnts csv in the data directory specifies the parameters that can be changed and used in a sample CDPOP run Open inputvariblesl6pnts csv in your editor of choice A spreadsheet program like Microsoft Excel allows for easy editing of the tabular values 3 There will be 3 lines of information in inputvariables csv a header line and 2 lines of information corresponding to 2 separate CDPOP runs batch process See the user manual pdf that contains a breakdown for each column header and the parameters that can be changed The Input in the table listed is for the F first row in the file Make sure you save this file in the same format a comma delimited file when you make changes to the parameters Select Yes or OK for any Excel questions about saving in this format E 4 Start the program For example if you use python from the command line then open a terminal window and change your shell directory to the CDPOP src home directory i e gt cd C homedirectorylocation src 5 Run the program There are a number of ways to r
8. EPD accepting defaults for the installation directory On Windows this will typically place the executables and libraries in c Python2 7 bin and the site packages package tree for user installed Python modules in c Python2 7 1ib 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 Note that if you choose EPD that you do not need to additionally install NumPy or SciPy 2 2 2 Install CDPOP Next install the CDPOP software itself by unpacking the zip archive supplied Navigate to the directory on your PC where you wish to install CDPOP and unpack 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 Simulations outside of any folder that has spaces in its name like My Documents At this point you should be able to execute th suppli
9. EVOLVE Answer is 2 then ng viability E ace for aaBb f ng has aaBb pl mortality fitness s used then this urface is Fitness AAbb Fitness AAbb Fitvals0 When CD this is EVOLVE the offspri Answer is 2 then ng viability selection surface for AAbb If offspri ng has AAbb E mortality fitness s used then this urface is Fitness Aabb Fitness_Aabb Fitvals0 When CD this is the offspri EVOLVE Answer is 2 then ng viability F selection surface for Aabb If offspri ng has Aabb E mortality fitness s used then this urface is Fitness aabb Fitness aabb Fitvals0 When CD this is EVOLVE the offspri Answer is 2 then ng viability F selection surface for aabb If offspri ng has aabb mortality fitness s used then this urface is CDINFECT cdinfect SN x turned off This is the infection parameter answer This tracks vertical transmission in the population A column in grid csv denotes the infection status at each CDPOP user manual 27 generation for every individual If Y then a random status infection 0 or 1 is created and initialized for each individual If N then the status 0 is created
10. Molecular Ecology Resources doi 10 1111 3 1755 0998 2011 03075 x d 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 or consequential damages arising from the use of or the inability to use this program 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 ecolo gy issues Therefore we do not wish to spend a great deal of time consulting on trivial matters concerning the use of CDPOP However we do recognize an obligation to provide some level of information sup port Of course we welcome and encourage your criticisms and sugges tions about the progra
11. be labeled genepopgrid generation txt 7 Output Files Folders will be created in your project directory label unique time stamp Monte Carl batch run folder you wil individual s genotype Mother and Father ID infection status additional In addition Monte Carlo run dos co o runs will will be uniquel sp a These ar generation e Year Th generations Populatio specify s then this Lly see the format fol n The total field will CDPOP user manual 30 ed with a atial locations and Pop it dispersed unique rom F ll see grid generation csv files that list each ID Time of birth age sex and The following is a summary of E If you specified a grid format option lowed by grid generation csv F each calculation total pop the subpopulation sizes in order ToTFemales Th you specify subpopul file then this fiel population in each generation ubpopulations in the first column of be separated by Vs total number of females in each generation If you your xy csv file The first value is the ulation size and each additional value corresponds to nvention e g 1332964297batchrunOmcrun0d be uniquely labeled mcrun0 mcrunl and each y labeled batchrun0 batchrunl In each then you will n output csv is automatically created for each ba
12. for each genotyp is under selection For example th be specified for the three genotype alleles A and a Selection is impl survival of dispersing individuals fitness at the location on that sur individual settles location specific fitness values fo pre processing step The program wi same as CDPOP with an additional s dispersal process F E Simulating dynamic landscapes The on the connectivity of populations among scientists and land managers and spatially explicit predictions n Mendelian reproduction In irs are one male to possibly many e end of the mating process occurs when all can have a number of offspring dom draw based on a uniform probability E pecified mean or a constant k allele mutation rate chosen by ffspring s genotype and the sex the mother s x y location function and the sex of the and death define whether or not or immigrants versions of CDPOP modeled three flow genetic drift and mutation nt genotypes have an equal g on their alleles to f future tion was not operating CDPOP V 1 0 ously to the adaptive or fitness ight 1932 This new functionality tic analyses to explicitly flow and selection in complex The user specifies fitness e of a single diallelic locus that ree relative fitness surfaces must s AA Aa and aa from the two emented through dif F
13. functionality is Simultaneously i e sensitivity anal provided through batch capability The simulation program assumes constan each locus for each individual can be F t 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 F initialized by randomly choosing F reading in a file containing the initi rom a file containing allel frequencies for each locus or by al multi locus genotypes of all the individuals The initial age structure of the population is initial age frequency The sex specified by an input file specifying of each initial individual is randomly assigned There are five movement functions that define how individuals choose a F mate and disperse on the landscape as a function of cost distance ential nearest neighbor and linear inverse square negative expon individual moves to the available grid randomly chosen from the n grids in th inverse square and negative exponenti individuals move a distance from their E random mixing With the nearest neighbor movement function an location nearest its initial location Random mixing moves an individual to a grid location that is e population In linear al movement functions initial location based on a F
14. individuals within as 1 Cost Distance j 2 Gaussian function A exp Cost Distance B 2 2 C 2 This function gets rescaled to min and threshold of the gaussian function cost distance 7 8 Use the cost distance matrix rescaled to the min and threshold Mating Movement Parameter A matemoveparA 0 0005 This is the A parameter used for the function in movement answer 5 Ts VB CDPOP user manual 16 atin ove Para 3 5 matemoveparB 0 01 This is the B parameter used for the function in movement answer 05 NTE NBA ovem Para 3 matemoveparC 300 01 his is the C parameter used or the function in movement mh H g e e ating e e g atin ovement Threshold matemovethre sh 5 swer 8 threshold option in cost istance units for how far an ndividual can search for a mate equivalent to the cost distance kernel You can specify max to consider all individuals for mating movement You can also place an 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 You can also just specify a specific cost distance value PO Female Replac
15. then this F mortality fitness surface is used Fitness Fitness AaBB Fitvals0 When CDEVOLVE Answer is 2 then AaBB this is the offspring viability CDPOP user manual 26 selection offspri surface for AaBB f E mortality fitness s used ng has AaBB then this urface is Fitness aaBB Fitness_aaBB Fitvals0 When CD this is selection sur offspri EVOLVE the offspri Answer is 2 then ng viability F ace for aaBB f ng has aaBB F mortality fitness s used then this urface is Fitness AABb Fitness AABb Fitvals0 When CD this is selection sur offspri the offspri EVOLVE Answer is 2 then ng viability P ace for AABb f ng has AABb F mortality fitness s used then this urface is Fitness AaBb Fitness AaBb Fitvals0 When CD this is selection sur offspri EVOLVE the offspri Answer is 2 then ng viability F ace for AaBb T ng has AaBb Pai mortality fitness s used then this urface is Fitness aaBb Fitness_aaBb Fitvals0 When CD this is selection sur offspri the offspri
16. 1 then Aa this is the offspring viability E selection surface for Aa offspring has Aa then this THe P mortality fitness surface is used Fitness Fitness aa Fitvals0 When CDEVOLVE Answer is 1 then aa this is the offspring viability E selection surface for aa offspring has aa then this mortality fitness surface is used TEE The following are the fitness surfaces for when CDEVOLVE Answer is 2 This corresponds to 2 loci that are under selection The x y location of an offspring is matched up with the closest x y fitness value for the offspring s corresponding fitness surface defined by the genotype that the offspring has That value then becomes the individual offspring mortality percentage An offspring becomes more or less fit relative to the other offspring at that generation as a function of its genotype and where it occurs on a surface These are ASCII formatted files with 6 lines of header information and values that are space delimited and represent percent mortality 0 100 See fitvals txt for an example fitness surface and its format Examples for uniform and gradient spatial selection files are given Fitness Fitness AABB Fitvals0 When CDEVOLVE Answer is 2 then AABB this is the offspring viability selection surface for AABB f offspring has AABB
17. CDPOP user manual 1 CDPOP USER MANUAL 2013 Version 1 2 21 Last Updated 2014 07 23e11 Contributors E L Landguth J M Glassy S A Cushman M Jacobi T J Julian B K Hand Allen Warren 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 I gt AMECLOQUELLON hi A AA A Sie Ee eed eae and ered ers 3 Ll Changes trom CDPOP VO spa eae a tees Ses a eae eee 3 t27 What Can CDLOP do iets fe sie ie Ge OOS Seat ew RN ee ee wd Se ee ree 3 123 How does lt CDPOP WORK siii iS dares awe wea owes 4 2 Getting Started its is el el GS wld nd WAS Ae A pea A 7 2rd DEPENGENCLES 4 ernes Sik eee ORAM E E E EEE ee es 2 1 1 Baseline requirements 2 122 EYyeaon On nOn wIindows platos snes dias a Ye 2 4 4253 PYTHON On WINAOWS se sats li le 2 lt 4 0btainang NumPy and SEL Y 2 dees ewis ees Les 262 Tnstaltat ron o cht ot ie tae te tie bt ante JA hy Mi ah Ne ce MG ita 2 2 1 Installing Python NumPy and SciPy Zi Za 2 Instaldang CDPOP 6 a Ver 2 abe 2 22 23 DESCETPELON OF EDROD TIMES a Berens cee Obey E 23 HB KAMP LS PUM gis ie ences a A es SS eth a eb ta 2003 Command LENS CUA ii a Snes 3 DP
18. DPOP user manual 24 It is basically a column of allele frequencies and make sure the length of the column equals your starting loci starting alleles Option multiple allele frequency distributions for each subpopulation Make sure intgenesans equals file Then a separate allel frequency file can be entered for each subpopulation given E g in the XY file if 4 subpopulations were designated in the first column and separate allele frequencies ar wished f for each of these populations then enter in the file name f for each subpopulation separated by a I e g Y allelefrequencyA csv random al lelefrequencyB csv random Note here that a file or random starting can be used Alleles alleles BA The number of starting alleles per locus mtDNA Mtdna VN If Y then last locus becomes mtDNA and every offspring inherits this locus from its mother only If N then regular Mendal inheritance occurs for this last locus CDEVOLVE Answer cdevolveans This is the answer for how many loci are under selection Use N to turn off CDEVOLVE Use 1 for natural selection with 1 locus Use 2 for selection with 2 loci Alleles must be 2 if Y is entered Burn in Ge
19. DispDiststd The standard deviation Euclidean distance individual offspring disperse from their natal location female and males for both as a as a MateDiststd The standard deviation cost distance probability individuals travel to mate DispDiststd The standard deviation cost distance probability individual offspring disperse from their natal location for both females and males P1 This is the allele frequency of A used for CD EVOLV E P2 TRIS ql This q2 This SubpopImmigration the ordered subpopulation CDPOP user manual 32 E E E is the all frequency of a used for CDEVOLV is the all frequency of B used for CDEVOLV is the all frequency of b used for CDEVOLV The number of individuals that immigrate to number Separated by YAE SubpopEmigration The number of individuals that emigrate from the ordered subpopulation Infected The number o number Separated by F H Aaa ndividuals that are infected at each generation used for CDINFECT with given transmission probility vertical infection FemalesMeanMate The mean number of females matings in a generation MalesMeanMate The mean number of male matings in a generation FemalesSDMate The standard deviation i
20. F erential as a function of the relative where the dispersing F Lac CDPOP v1 2 reads and extracts genotype and r each n x y individual in the 11 continue all other processes the tep implement selection during the potential impacts of climate change have become an area of concern Current needs include quantitative of current and potential future patterns of fragmentation under a r Opdam amp Wascher 2003 To address to input a new landscape surface at ange of climate change scenarios this need CDPOP v1 2 allows users a given generation time through CDPOP user manual 6 new cost distance matrices for both mating and dispersal Simulating demographics CDPOP v1 2 now allows for fluctuating population sizes controlled by birth rate death rate carrying capacity and ability of offspring to disperse given a specified resistance surface The program is written in Python 2 7 and provided with installation instructions for most platforms along with sample input files CDPOP v1 2 is built on a driver module plug in docking architecture that allows for ease of future modular development CDPOP v1 2 has been debugged as carefully as possible by testing all combinations of simulation options Information for users including user manual FAQ publications ongoing research developer involvement and downloads can be found at http cel dbs umt edu software CDPOP
21. I E Gate A ah Gree od oA a See eS 12 Ar QUE DU ete a a a E AS ERRADA DA T a ana eee a alese d 28 5 General ISSUES eit tase is oa eee ha ad ada 31 Diy A HOW OOD Pain CDROPD sw tai ae tee Mush ine bea eee inmate doe Daya Diz Debugging and EroubleshootinBui idaho 55 3 How to cite CDPOP 5 4 DaAsClLaARMe Pie 6 wht teow wos Sate Sh aoe lS SSS DEAS wi we etre E Referentes eere Seabee A Al Ai 32 7 Acknowledgements 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 2 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 There are major innovations in v1 2 which were not included in the previously published v0 70 We list below the new functionalities of CDPOP v1 2 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 c
22. a unique date time stamp after the name of the output folder in case you want to run multiple CDPOP runs in this same directory The program will also provide a log file with program steps in your specified output directory If parameters are such that population becomes extinct before specified generation time then program will end 3 Input The foll CDPOP are for each fil See exan CDPOP user manual 12 owing are the general input parameters and files used in nples provided for F the GUI le or parameter and the first row ormatting Th in the inputvariables csv describing file headers listed The example provided is for the first line in the inputvariables csv file File Header File Header Example Description in GUI in csv XY Filename xyfilename xyED16 example The n x y grid location supplied for 16 values This is a comma individuals delimited file with 5 column headings xyED16 NAs csv gives you an Subpopulation a unique example of how to identifier for each individual specify your corresponding to a unique initial starting subpopulation This is an population size optional tracker for This example is 16 individuals that may be located possible habitat in designated subpopu
23. alculated E nter braycurtis for the Bray Curtis distance measure Dps for the proportion of shared alleles or Da for Nei s genetic distance F Specify N here if you do not want to calculate these matrices Note that Nei s genetic CDPOP user manual 29 distance takes the longest to calculate and may decrease your total CDPOP simulation time All are slightly expensive in computation time and we are working on speeding these up Genotype Output Format gridformat genepop This is the genotype output format option The format for the genotype output is E specified by entering cdpop This format is the default The cdpop format lists the genotypes with values f for each allel gt elthet 0 1 or 2 Output will be labeled grid generation csv F general for a general genotype output The general format will ollow Locusla Locuslb Locus2a Locus2b LocusNa LocusNb Output will be labeled generalgrid generation csv E genalex for the program GENALEX Output will be labeled genalexgrid generation csv structure for the program structure or related programs Output will be labeled structuregrid generation stru genepop for the program GENEPOP or related programs Output will
24. cal bar Sequence of Generations Saved nthfile seq 1 will save the sequence of genotypes for grid0 csv gridl csv grid4 csv The specified simulation run time to write to file and to calculate 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 A value of 5 would output every 5 generation etc CDPOP user manual 15 Mating Movement Function matemoveno 1 linear probability function of mating cost distance Movement function answer for mating probability 1 Linear 1 1 Threshold Cost Distance 2 Inverse Square 1 Cost Distance 2 This function gets rescaled to min and threshold of the inverse square cost distance 3 Nearest Neighbor Use threshold to specify Moore neighborhood 4 Random Mixing and will consider the cost distance threshold Use the maximum cost distance in the threshold field if you want to consider the entire population as random movement 5 Negative Exponential parA 10 parB Cost Distance This function gets rescaled to min and threshold of the negative exponential cost distance 6 Subpopulation Given the subpopulation j then movement will occur using the cost distance matrix of
25. draw from a probability distribution i nversely proportional to a linear inverse square or negative exponential function The user specifies the maximum dispersal dis can travel on the landscape The pr CDPOP user manual 5 tance in cost units an individual obability is one at no distance from the original location and goes distance F Reproduction is defin heterosexual but individuals mate ed by the user With hermaphroditic mating with other individuals according to the movement to zero at the maximum dispersal as either hermaphroditic or there are no distinct sexes function choice exch heterosexual reproduction or no females and th females have mated E that is a bounded ra distribution a Poisson draw with s number Mendelian inheritance with the user is used to generate the o assignment is random anging genes i mated pa ach mated pair Dispersal of offspring occurs from according to the selected movement individual The vital rates birth the population will have emigrants Simulating natural selection Past sources of genetic variation gene These versions assumed that differe probability of surviving and passin generations and thus natural selec implements natural selection analog landscape of all frequencies Wr nables extension of landscape gene investigate the links between gene landscapes at an individual s level landscape surfaces
26. ed test inputs 2 2 3 Description of CDPOP files 3 directories will be installed in your directory Here is a description of each 1 src CDPOP source code 2 doc gt README txt a quick how to run CDPOP instructions gt CDPOP user manual pdf this file gt CDPOP history txt Notes on history and version changes 3 data Example input files gt Edcdmatrix16 csv example Euclidean distance cost distance matrix file gt xyED16 csv example n x y file for individuals gt xyED16 NAs csv example n x y file with sparse individuals gt xyED16 known csv xample n x y file with known genetic data gt agedistribution csv example age distribution file CDPOP user manual 9 F allelefrequency csv example allele frequency distribution gc ile fitvals0 txt and fitvals50 txt example fitness landscapes for natural selection uniform spatial selection files with differential mortality corresponding to 0 and 50 gradient4x4 N23 S66 txt gradient4x4 N50 S50 txt and gradient4x4 N80 S20 txt example fitness landscape for natural selection gradient spatial selection files with differential mortality from North to South at 23 66 50 50 and 80 20 respectively inputvariablesl6pnts csv run parameters corresponding to the example files CDPOP user manual 10 2 3 Example run 2 3 1
27. ement Freplace N females mate without replacement F If you want females to mate with replacement then specify YEN females to mate then If you want without replacement specify N Male Replacement Mreplace Y males mate with replacement f you want males to mate with then specify Y replacement If you want males to mate without replacement then specify N Multiple Paternity Answer multiple pat ernity y females can have a litter from multiple males If you want multiple paternity with birth rates applied the same for each female with litter then specify Y If you want multiple paternity with birth rates applied unequally for each female with litter then specify N F This answer is only functionly when Freplace Y and Mreplace Y or multiple paternity option The CDPOP user manual 17 difference is subtle For example if the birth rate is set at a constant litter size offno 3 of 2 lambda 2 and multiple paternity Y then if a female mates with 2 males the female would have 2 offspring 1 from each male However if multiple paternity N then if a female mates with 2 males then that female would have 4 offspring Selfing Answer Selfans SN
28. for all individuals and initialized Transmission Probability Transmission prob Ogay This is the transmission probability for if a parent has the infection the chance that the infection will be passed along to the offspring CDCLIMATE cdclimate N changing cost distance matrices turned off This is the dynamic landscape answer If Y then a new cost distance matrix will be read in at a specified generation time in the next column TE ON used then this option is not CDCLIMATE Generation Cdclimgentim e valo The generation time that the next cost distance matrix will be read in at You can specify multiple generations by separating each generation to read in the next cost distance matrix by Future Mating CD Matrix Futuredispcm at 2 E EDcdmatrix16 DCdmatrixl6 A nxn future cost distance matrix for mating movement where n is the number of grid values or individuals on the landscape 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 If you are using multiple surfaces i e you specified multiple cdclimate generations by separating them with then you will also need to specify multiple cost distance matrices here as well by using a
29. hilopatry For example if this is specified for female philopatry F then females will be able to remain in their birth locations If this is turned off N then males have the chance of coming into a female territory and taking it over When N is specified then the generation will produce equal female and male occupied locations This option will only work with a unique combinations of parameters with each philopatry combination For example for female philopatry F female dispersal threshold must be 0 no movement You must start off with initialized equal sexes You must specify equal sex ratio AtBirth You must specify female mating without replacement You must use male movement 1 2 5 or 6 CDPOP user manual 20 For M use male dispersal 0 equal sexes initialized AtBirth sex ratio and either female movement rules 1 2 5 or 6 Offspring Choice Offno 12 Poisson distribution This is the number of offspring each mate pair can have 1 for a random draw 2 for Poisson draw 3 for a constant number of offspring 4 for an equal clutch size for each female Note that option 1 3 will assign a clutch size to each mate event For example if a female mates with 4 males and offno is set to 3 with lambda of 2 then she will have 8 offspring Option 4 wi
30. is file Also note that this file can be calculated from any program you choose e g PATHMATRIX CIRCUITSCAPE UNICOR COSTDISTANCE etc It can be the same file as the Mate CD Matrix Monte Carlo mcruns 5 5 replicate The repeated number of Replicates runs denoted in Simulations to be conducted for folders labeled the Monte Carlo method i e with mcrun0 the number of replicates for 1 merun po batch of parameters Generation T Looptime ELOY gt 10 Simulation run time generation ime generations or year File output indexed from 0 looptime 1 For example grid0 csv gridl csv grid2 csv grid3 csv and grid4 csv would be outputted for a looptime of 5 Generations nthfile choi Sequence will The choice of a specified of Saved ce save a specified simulation run time Genotypes sequence of generation to write to file Choice generations and to calculate genetic distance matrices List read nthfile list values below Sequence read nthfile seq value below List of nthfile list 0 3 4 the list The specified simulation run Generations of generations to time to write to file and to Saved save and here calculate genetic distance cdpop would save grid0 csv grid3 csv grid4 csv and matrices These values are used if nthfile choice List These values must be separated with a verti
31. lations locations that can If individuals are just be filled with continuously distributed then only 11 fill with arbitrary value like initialized with 1 If these field is used individuals You then subpopulations must be in must specify NA sequence e g 1 2 3 values in the ID and sex columns XCOORD x coordinate location but still provide the xy locations YCOORD y coordinate location that are OPEN and YCOORD a Supopulation identifier field ID a string label identifier and sex an initial sex assignment use 0 1 or F M See xyED16 csv for an example xyfilename The column order is necessary and header file included See below for specifying constant versus non constant population sizes Age agedistribut N no age The distribution that is used Distribution ion distribution file to initialize each individuals Filename is used and age is age initialized at 0 for all N no file is not used and indidivuals age initialized with 0 CDPOP user manual 13 Filename 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 and note it must be comma delimited The file includes two columns the Age class start initial age of offspring as 0 and Number in age class which is the number of individuals in each cla
32. ll assign a clutch size to each female that mated For example if a female mates with 4 males and offno is set to 4 with lambda of 2 then she will have 2 offspring total and the father s is randomly selected from the 4 mating events Lambda Lmbda 5 Poisson distribution with mean lambda 5 The parameter value used with Offspring Number If offno 1 then lmbda is the max range value between 0 imbda to draw randomly from If offno 2 then lmbda is the Poisson mean for the litter size If offno 3 then lmbda is the constant litter size value Female offspring Femalepercen E 150 50 random female assignment Percent number of female born in each litter This is a random assignment from given percentage i e even if you CDPOP user manual 21 set this to 50 some generations could have 499 female births and 501 male births for example Equal Sex Ratio for Offspring Equalsexrati oBirth N This ensures an exact equal sex ratio for the following options WrightFisher The answer to hav very generation start with equal sex ratios CAREFUL this parameter is not realistic for non panmictic populations and should only be used to match Wright Fisher assumptions on equal sex ratios AtBirth
33. lumn of The each additional This is the number of breeding events for females This number times the birth rate will give the total number of births in that generation Females NoMate a mate Migrants The it to the next DisperseDeaths This is the number of females that did not have number of dispersers in each generation that make generation The number of dispersers in each generation that do not make it to the next Births E The number of of CDPOP us generation er manual 31 spring born at that generation AdultDeaths The number of deaths of the adult population the offspring born that ye not bau fa ar generation The apping generations for th age class deaths for over class in that generation age classes and not report Alleles This is the tota generation This value can separates th ordered ag Note that some years may not have all ed number of unique allel be calculated automatica s at each lly for specified subpopulations if different subpopulations were 21 designated in the initial first value corresponds to xyfilename If there are the total alleles in the ollow after and subpopulation values f He This is th generation This value can be calculated automatica alee then the population xpected heterozygosity value at each lly for specified sub
34. m at all times We will welcome questions about how to run CDPOP or interpret the output only after you have read the entire documentation This is only fair and will eliminate many trivi al questions Finally we are always interested in learning about how F CDPOP user manual 34 others have applied CDPOP in ecological investigation and management application Therefore w ncourage you to contact us and describe your application after using CDPOP We hope that CDPOP is of great assistance in your work and we look forward to hearing about your applications Shiny 9 References Allendorf F W and Luikart G 2007 Conservation and the genetics of populations Blackwell Malden MA Bowcock A M et al 1994 High resolution 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
35. n the number of females matings in a generation variance in reproductive success MalesSDMate The standard deviation in the number of male matings in a generation variance in reproductive success OpenLocations The number of habitat avail did not get filled during dispersal CouldNotDispers Th individual number of able locations that s that could not disperse due to high cost to moving to an open locations CDPOP user manual 33 8 General issues a How to obtain CDPOP The program is freeware and can be downloaded at http cel dbs umt edu software CDPOP with information for users including manual instructions FAQ publications ongoing research and developer involvement b Debugging and troubleshooting For help with installation problems please check first for postings at our web site Otherwise please report problems including any bugs to me at erin landguth mso umt edu c How to cite CDPOP This program was developed by Erin Landguth with help from Brian Hand Joe Glassy Sam Cushman and Tyler Julian GUI development was done by Mike Jacobi The reference to cite is as follows substituting the version number Landguth EL Cushman SA Jacobi M 2010 CDPOP A spatially explicit cost distance population genetics program Molecular Ecology Resources 10 156 161 Version X Landguth EL Cushman SA Johnson NJ 2011 Simulating natural selection in landscape genetics
36. neration Burningen 10 This is the generation or year that the selection surface will begin operating on the locus or loci under selection specified in previous field CDPOP user manual 25 cdevolveans If N is specified for cdevolveans then this field is ignored The following are the fitness surfaces for when CDEVOLVE Answer is 1 This corresponds to 1 locus that is under selection The x y location of an offspring is matched up with the closest x y fitness value for the offspring s corresponding fitness surface defined by the genotype that the offspring has That value then becomes the individual offspring mortality percentage An offspring becomes more or less fit relative to the other offspring at that generation as a function of its genotype and where it occurs on a surface These are ASCII formatted files with 6 lines of header information and values that are space delimited and represent percent mortality 0 100 See fitvals txt for an example fitness surface and its format Examples for uniform and gradient spatial selection files are given Fitness Fitness AA Fitvals0 When CDEVOLVE Answer is 1 then AA this is the offspring viability selection surface for AA offspring has AA then this TE F mortality fitness surface is used Fitness Fitness Aa Fitvals0 When CDEVOLVE Answer is
37. omplex landscapes on the genetic structure of populations e Demographics allows for fluctuating population sizes FE e Sex specific 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 with giving probability e mtDNA option e Output genotype option in multiple formats genalex structure genepop general e Generation can be specified to change landscape surface for both mating and dispersal e g climate change scenarios e Subpopulation differential mortality An individual can be given an increased mortality if it disperses to another subpopulation e Philopatry option added for both male and females e Multiple paternity option added i e females can have litters from multiple males but birth rate is same for each female e Additional mutation models added step wise forward and backward e Age structured mortality added for overlapping generations e Burn in procedure options 1 2 What can CDPOP do CDPOP s realistic representation of th e spatial CDPOP user manual 4 environment and popu lation genetic processes provide a powerful framework to investigate e genetic struc
38. ows installer available from the SourceForge websit 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 We highly recommend this version for easy installs 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 11 get the python prompt gt gt gt If it is not a recognized 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 CDPOP user manual 8 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 ActiveState or
39. populations if different subpopulations were designated in the initial xyfilename If there are first value corresponds to subpopulation values follo the total w after Ho This is th generation This value can then the OR He in the population and observed heterozygosity value at each be calculated automatically for specified subpopulations if different subpopulations were designated in the initial xyfilename If there are then the first value corresponds to the total Ho in the population and subpopulation values follow after Mutations The total number of mutations at each generation MateDistED The average Euclidean distance individuals travel to mate DispDistED The average Euclidean distance individual offspring disperse from their natal location separated into female and male movement MateDistCD The average cost distance as a probability individuals travel to mate This can be converted back to cost distance if using a linear function DispDistCD Th individual average c ost distance into female and male movem ent as a probability offspring disperse from their natal location separated This can be converted back to cost distance if using a linear function MateDiststd The standard deviation Euclidean distance individuals travel to mate
40. special case for the 2 loci selection model The first locus under selection can only go forward A gt a and the second locus under selection can only go backward b gt B The rest of the neutral loci are random mutations Loci loci The number of loci microsatellites Initialize Genotypes intgenesans The choice for how to initialize the genotype for each n x y individuals If random is entered 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 THe known is entered then th genotypes are directly read from a given known file This file is very similar to the initial xyfilename and example XyED16 known csv is supplied with test data files Allele Frequency File Allefreqfile name frequency 1 The allele frequency distribution for each locus used to initialize the model s n individual s genotype If you want to use a frequency distribution file you must set Initialize Genes Answer to equal file and then enter in the filename in this field See allelefrequency csv example file for formatting this file C
41. ss Option multiple age distributions for each subpopulation A separate age distribution file can be entered for each subpopulation given E g in the XY file if 4 subpopulations were designated in the first column and separate age distributions are wished for each of these populations then enter in the file name for each subpopulation separated by a 11 e g agedistributionA csv N agedist ributionB csv N Note that N can be used in this list as well Mate CD matecdmat EDcdmatrixl6 A nxn cost distance matrix Matrix an example for mating movement where n is Filename Euclidean distance the number of grid values or matrix used for individuals on the landscape the mating This is a comma delimited file movement S th xampl EDcdmatrixl6 csv for formatting this file Also note that this file can be calculated from any program you choose e g PATHMATRIX CIRCUITSCAPE UNICOR COSTDISTANCE etc Dispersal CD dispcdmat EDcdmatrixl6 A nxn cost distance matrix Matrix Filename an example Euclidean distance matrix used for the dispersal E or dispersal movement where n is the number of grid values or individuals on the landscape This is a comma CDPOP user manual 14 movement delimited file S th xample EDcdmatrixl6 csv for formatting th
42. st distance See Mating Movement Choice dispersal ale Mdispmovepar 1 This is the A parameter used Dispersal A for the function in movement ovement answer 5 V Parameter ale dispmovepar 1 This is the B parameter used Dispersal B for the function in movement ovement answer 5 V Parameter ale dispmovepar 1 This is the C parameter used Dispersal C for the function in movement ovement answer 7 Parameter ale Mdispmoveno max will A threshold option in cost CDPOP user manual 19 Dispersal Movement Threshold travel th HELY landscape as an inverse square probability of cost distance on F the surface distance units for how far an individual male offspring Can disperse You can specify max to consider all individuals for mating movement You can also place an 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 F distance on the surface You F can also just specify a F specific cost distance value Philopatry Philopatry ANA turned off philopatry Ye This is the behavior of remaining at the individual s birthplace The options are N turned off F Female philopatry M Male p
43. st mortality category F Subpopulatio n Mortality Subpopmortpe re OOTO TO This parameter is the percent mortality for a dispersing offspring into another subpopulation Each subpopulation gets separated by a and has it s own percent mortality For example if an offspring was born in the second subpopulation and disperses to the fourth subpopulation it has a 60 chance of surviving there If it stays in its own subpopulation then it would have no differential mortality consequences This parameter is very similar to cdevolve offspring viability but applied to subpopulations instead of individuals spatial locations Mutation Rate muterate 0 0005 The mutation rate Mutation Model mutationtype random model the KAM The type of mutation model random This is the kth allele mutation model forward This is a step wise mutation in which an allele can mutate forwards only i e to the right backward This is a step wise mutation in which an allele can mutate backwards to the left only i e forwardbackward This is a step wise mutation in which an allele can mutate forward or CDPOP user manual 23 backwards only i e to the left or right with equal probability forwardAbackwardBrandomN This is a
44. tch and e population based metrics calculated at each is is the generation time or year if using overlapping If Lations in the first column of your xy csv d will is the total female the subpopul ation sizes be separated by nE keg The first value size and each additional value corresponds to in order ToTMales The total number of males in each generation specify subpopulations in the first col then this field will subpopulation sizes be separated by total male size and each additional Mv val in order BreedFemales Th generation your xy csv file first value is the total value corresponds to the subpopulation sizes in BreedMales Th generation your xy csv file Br dEvents total If you specify subpopul then this field will number of lations in th breeding F a F umn of your xy csv f you ile The first value is the ue corresponds to the A be separated by order lations in th 1 ey be separated by size and order Fema breeding age females in each e first column of The emale size and each additional total number of breeding age females in each If you specify subpopul then this field wil first value is the total breeding male value corresponds to the subpopulation sizes in e first co
45. ture of popula the impact of ecological factors on th tions This approach has already advan ced know ledge of the patterns of genetic variation in spatially explicit contexts Landguth et al 2010a Landguth et al 2010b Cushman and Landguth 2010 Landguth and ave included Balkenhol 2012 Example simulations h e Quantifying the time to detect barriers e Correlating migration rates and landscape resistance barriers e Testing for the effects of population sample size and number of markers e Assessing relative influence of adaptive versus neutral markers in detection of population genetic differentiation 1 3 How does CDPOP work CDPOP vl 2 models genetic exchange for a given resistance surface and n x y located individuals as func tions of individual based movement through mating and dispersal E interface or input script file As the processes most applications will quan genetic structure across many runs Th F single set of input parameters In add vital dynamics and mutation A user must specify the input parameters through a graphical user model simulates stochastic tify mean and variability of us a Monte Carlo option is provided for the user to choose the number of runs to simulate given a ition a user may also frequently wish to launch several runs with different parameter values ysis This
46. un this program If you are using a command shell you can run the program by typing python CDPOP py C homedirectorylocation data inputvariableslopts csv output_test Note that there are 5 arguments here that must be included with spaces in between gt python starts python for example from the command line Note that other python environments may have different calls here In PyLab the IDE distributed with EPD the call is SEUR g gt CDPOP py runs CDPOP program gt C homedirectorylocation data is the directory location of the input test files You can point this directory to other project files for example We suggest not having any spaces in your directory names gt inputvariablesl6 pts csv is the parameter file gt output_test is the name of the directory that will be created with CDPOP output in the directory specified by the third argument above YA CDPOP user manual 11 Check for successful model run completion The program will provide step by step output in the Shell window Once completed a simulation time will be printed out and folders batchrunOmcrunO batchrunOmcrunl batchrunOmcrun2 batchrunOmcrun3 batchrunOmcrun4 and batchrunlmcrun0O will be created in your CDPOP home directory to store output from the separate batch and or Monte Carlo runs These folders are located in the data folder specified in above step The output folder will have
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