USER MANUAL - Computational Ecology Laboratory
Contents
1. 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 among samples Molecular Ecology Notes 5 177 180 11 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 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 05046282. These values must be separated with a vertical bar Nthfile Sequence 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 CDPOP user manual 12 of 5 would output every 5 generation etc Adult Percent mortality in the adult population Mortality 100 Use 100 here to specify non overlapping Percent generations 3 3 Mating parameters The following lists the parameters used for the movement of individuals due to mating File Header Example Description ab ovement function answer for mating 1 Linear 2 Inverse Square 3 Nearest Movement 1 ee Neighbor 4 Random Mixing and 5 Negative Number ore Exponential ate pe s eee This is only used for negative exponential y Movement Pie g a 10 bx and is the parameter a parA ate i 5 E i ee This is only used for negative exponential y Movement he i 2 a 10 bx and is the parameter b parB A threshold option in cost distance units for how far an ind
3. 1 This GUI has a dependency on the python library WXpython Go to http wxpython org download php and download install your OS s version of WX python Download and unpack the cdpop gui zip This is a separate download file located under the CDPOP downloads located online Put all files in the same home directory where you installed CDPOP CDPOP user manual 9 3 Start the interface a Navigate to CDPOP home directory b Double click cdpopi py MM CDPOP User Interface Variables CDINFECT Track infection Transmission proba CDCLIMATE 4 Change surface Generation to chan Future mate surfac lEDedmatrix16 Future dispersal s EDedmatrix16 5 Submit Batch s 4 Guide the interface a Clicking File brings down a drop down menu with About and EXIT e About This presents a pop up dialogue of information about the version and developers of CDPOP e Exit Quits the program Work is not saved To prevent lost work click Submit Simulation before exiting the program b Radio buttons are listed next to each variable Only one radio button can be selected at a time When selected the Infor mation panel on the right half of the interface displays re lated information to the associated variable C These are input fields There are text input fields and drop down input fields The default values for each variable are autom
4. Sh we CRS ele So ieee dee as 8 Br AUB PA ates Bae SA A A coos A ar A ths ahd eet ea 10 31 Input File S ta Oke a E A a ae ate ee ES 10 322 Model Parameters dras sais a Piven A A de a 11 3537 Mating ParameterS iii sata ad 11 3 4 Dispersal Parameters es a a da 12 325 OFPSPrIng Parameters io a aa sado dy dadas 13 3 50 Genetic Parameters i se chan a A eee Pes 13 Sal EDEVOLVE 42 a a aida Oa LS 3 8 CDINEEG Pirene AS A AA A AR E a ee hate LY 359 EDELIMATE tt ws totter a a a e A aa co he tan iaa ds 17 4 Output A OS A A A A eas a eh A he GS Si aes 18 4 Individval based OQUEPput ETS Sia a be oe sti ers ER gi Se 18 4 2 Population based Output File Secs se ck eee ee ais wees 18 5 General ISSUE a Sire ews es ae 20 Sel HOW to ObEALA CEDRO Brisa a Wer el ea eas 20 5 2 Debugging and troubleshootiNnG oooooooooo ooo ee eee 20 53 HOW EO CTES CDPOPR cae il a e ds a 20 6 Referentes darse saco aia aa e He sce wh Swi eR a a ot ole ai aoa ew ew a 21 TP AcknowledgementS cs a Bae we Roe Ra ei ee we 21 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 bre
5. l 5 10 specify multiple generations by separating Generation each generation to read in the next cost distance matrix by 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 da ED format Note that this file must be the same Matin cdmatrixl6 size as the initial cost distance matrices g ED used in the simulations If you are using CDMatrix AS p Dia Cdmatrix16 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 CDPOP user manual 18 Future Dispersal CDMatrix dispersal grid values landscape ED cdmatrixl6 ED Cdmatrixl16 size as the used in the multipl SUL A nxn future cost distance matrix for movement where n is the number of individuals on the or This is a comma delimited file format Note that this file must be the same distance matrices If you are using you specified initial cost simulations faces i e multipl them with F A as well e cdclimate generations by separating then you will also need to specify multiple cost distance matrices here by using a Me 4 Output Files 4 1 Indi
6. used with the module CDINFECT Currently only nsmission is assumed Future development will include vertical tra horizontal transmission parameters This a beta test module File Header Example Description CDINFECT This is the infection parameter answer This tracks vertical transmission in the population 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 for all individuals and initialized A column in grid csv denotes the infection status at each generation for every individual Trans mission Probability This is the transmission probability for if a parent has the infection the chance that the infection will be passed along to the offspring 3 9 CDCLIMATE These are the parameters that control the dynamic landscape functionality within CDPOP A generation time is specified and input cost distance matrices ar then read into the program and used in Simulations File Header Example Description This is the dynamic landscape answer If s r 4 CDCLIMATE N yer then a new OPPE Sator matrix WLLL Be read in at a specified generation time in the next column The generation time that the next cost distance matrix will be read in at You can CDCLIMATE
7. CDPOP user manual 1 CDPOP USER MANUAL 2011 Version 1 0 Last Updated 2011 06 16 Authors E L Landguth B K Hand J M Glassy S A Cushman M Jacobi and T J Julian 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 0btainang NumPy and SELL Y 2 AA os 6 22 scal latromas eigu e cht ot ie eae te tet ahaa JA hy Mi ah Ne den AG cie 6 Zidel taste Ling Python NumPy and SCLPY umm sas eek 6 Zi Za 2 Instaldang CDPOP eS a Vee abs 7 2 22 23 DESCETPELON OF EDROD TIMES a acl Berea eee Obey bok 7 2 3 aor PU A Bo eh aa a a ee 7 Sul Command Vane sy sates el Pa wile de akan bse eA A al aed 7 oSeZ GUE PUN ta ii
8. Modules py Python library with general functions FEF Offspring py Python library for the offspring functions PostProcess py Python post processing library PreProcess py Python pre processing library tribution csv example age distribution file frequency csv examp allele frequency distribution file s0 txt example fitness landscape for natural selection ariablesl 6pnts csv run parameters corresponding to the e files user manual pdf this file 2 3 Example run 2 3 1 Comman d line run The example run is CDPOP user manual 8 Y or 16 points representing individuals with a cost distance matrix calculated with Euclidean distance To run the E following example E ollow these steps Double check that the 15 files provided in the archive are in the same directory 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 It is in a comma delimited format each parameter is separated with a comma and this format can not be changed A spreadsheet program like Microsoft Excel allows for easy editing of the tabular values 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 Section 3 contains a breakdown fo
9. ae 0 CDEVOLVE Use 1 for natural selection with 1 locus Use 2 for selection with 2 loci Alleles must be 2 if Y is entered 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 When CDEVOLVE Answer is 1 then this is the Fitness Fitvals0 offspring viability selection surface for AA AA If offspring has AA then this mortality fitness surface is used Fitness When CDEVOLVE Answer Ls ly then this is the Aa Fitvals0 offspring viability selection surface for Aa If offspring has Aa then this mortality CDPOP user manual 16 fitness surface is used When CDEVOLVE Answer is 1 then this is the Fitness Fitvals0 offspring viability selection surface for aa aa If offsprin
10. atically entered d This is a Category header Related variables are grouped under common headers e Variable name Ident with CDPOP user manual 10 ifies what the input field is associated f Submits a batch of input A simulation may have 1 N number of batches Up Na Title of selected variable Detailed description of selected variable Shows number of currently submitted batches Submits the simulation with the number of batches shown 5 Use the interfac a Enter in your parameters defaults given are for the example input b Click files Submit Batch c Change parameters if Submit Batch d After satisfied with click Simulation in the r e A successful or uns in the left panel at bottom more batches are desired continuing to batch parameter options click Submit ight panel uccessful CDPOP simulation box will noti fy you and output will be stored in your home directory 3 Input 3 1 Input files The following are the general input parameters and files used in CDPOP See examples provided for formatting The file header listed is for the first row in the inputvariables csv describing each file or parameter File Header Example Description XY Filename xyED16 The n x y grid location values This is a comma delimited file with 5 column headings Subpopulat
11. ce movement Movement A i Threshold 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 Male This is the function answer for movement for Dispersal 1 male dispersal Linear 2 Inverse Movemen Square 3 Nearest Neighbor 4 Random Number Mixing and 5 Negative Exponential Male Dispersal 1 Used only for negativ xponential y a 10 ovement bx and is the parameter a parA Male Dispersal 1 Used only for negativ xponential y a 10 ovement bx and is the parameter b parB Male A threshold option in cost distance units i 10 whee f Dispersal for how far an individual male offspring can CDPOP user manual 14 Movement disperse You can specify max to consider Threshold 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 3 5 Offspring parameters The following lists the parameters that control offspring births and deaths File Header Example Desc
12. dscape that is user defined by the n each locus for each individual can be initial e co ntaining all ile containing the initial the individuals x y located individuals frequencies for each locus multi locus genotypes of all F The genotype o lized by randomly choosing or by The initial age structure of the population is specified by an input file specifying initial of each initial age frequency The sex individual Ther fiv Pai ar mate and disperse on the inverse square inear location randomly chosen from the n grids in the and negative exponential movement functio individuals move a distance from their rom a probability distribution inversel or negative exponential function inverse square F draw linear random mixing With th individual moves to the available grid movement unctions that define how individ landscape as a function o negative exponential nearest neighbor movement location nearest is randomly assigned uals choose a cost distance nearest neighbor and function an its initial E Random mixing moves an individual to a grid location that is popul ation In linear initial NS location based on a y proportional to a inverse square specif E distance Reproduction is de can travel on the landscape rom the orig
13. e average cost distance individuals travel to mate DispDistCD The average cost distance individual offspring disperse from their natal location Pl This is the allele frequency of A used for CDEVOLVE CDPOP user manual 20 h E requency of a used for CDEVOLVE requency of B used for CDEVOLVE requency of b used for CDEVOLVE e Infected The number o ndividuals that are infected at each generation used for CDINFECT e P2 This is the all e ql This is the all e q2 This is the all h h E Ju 5 General issues 5 1 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 5 2 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 5 3 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
14. eding and dispersal 1 1 Changes from CDPOP v0 7 There 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 E 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 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 e
15. ele frequency distribution file CDPOP user manual 15 specified in next column allefregfilename If known is entered then the genotypes are directly read from a given known file This file is very similar to the initial xyfilename but email Erin Landguth erin landguth mso umt edu for an example file to use for Known The allele frequency distribution for each locus used to initialize the model s n individuals genotype If you want to use a frequency distribution file you must set Aerie Initialize Genes Answer to equal file and N then enter in the filename in this field filename AS an See allelefrequency csv example file for formatting this file It is basically a row of allele frequencies and make sure the length of the row equals your starting loci starting alleles Alleles 10 The number of starting alleles per locus If Y then last locus becomes mtDNA and mtDNA N every offspring inherits this locus from its mother only If N then regular Mendal inheritance occurs for this last locus 31 CDEVOLVE The following lists the parameters and surfaces used to simulate natural selection File Header Example Description This is the answer for how many loci are CDEVOLVE under selection Use 0 to turn off e
16. ement where n is the number of grid values or individuals on the landscape This is a comma delimited file See the Mati ED example edcdmatrixl6 csv for formatting this cdmatrix16 file Also note that this file can be Filename gt calculated from any program you choose e g PATHMATRIX CIRCUITSCAPE UNICOR COSTDISTANCE etc It can be the same fil as the Mate CD Matrix 3 2 Model parameters The following lists the general model parameters used for CDPOP File Header Example Description Mcruns The repeated number of simulations to be conducted for the Monte Carlo method i e the number of replicates for 1 batch of parameters Looptime Simulation run time generation 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 Nthfile Choice Sequence The choice of a specified simulation run time generation to write to file and to calculate genetic distance matrices If List is entered then read nthfile list values below If Sequence is entered then read nthfile seq value below Nthfile List 0 3 4 The specified simulation run time to write to file and to calculate genetic distance matrices These values are used if nthfile choice List
17. g has aa then this mortality fitness surface is used 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 When CDEVOLVE Answer is 2 then this is the Fitness Fitvals0 offspring viability selection surface for AABB AABB If offspring has AABB then this mortality fitness surface is used When CDEVOLVE Answer is 2 then this is the Fitness Fitvals0 offspring viability selection surface for AaBB AaBB If offspring has AaBB then this mortality fitness surface is used When CDEVOLVE Answer is 2 then this is the Fitness offspring viability selection surface for 1 aes offspring has aaBB then this
18. g http www scipy org Download This NumPy and SciPy in your Python site packages directory 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 Seven Zip 7Z exe is highly recommended since it can handle all like 7Zip 7z exe Pkunzip Unzip or an equivalent 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 supplied test inputs 2 2 3 Description of CDPOP files 15 files wil each e README EDcdma matrix e xyED16 DPOP_ DPOP DPOP DPOP_ DPOP_ e agedis E C G C C C C e allele e fitval e inputv exampl e CDPOP 1 be installed in your directory Here is a description of txt a quick how to run CDPOP instructions trixl6 csv example Euclidean distance cost distance file csv example n x y file for individuals DPOP py Python driver code and run file Disperse py Python library for the dispersal functions GetMetrics py Python library for the metric functions DPOP Mate py Python library of the mating functions DPOP
19. he genotype output is specified by entering general general genotype output or cdpop genotype output fora cdpop for the The general format Locus2b ollow Locusla Locuslb Locus2a LocusNa LocusNb The cdpop format lists the genotypes with values for each allel gt On 2 1ther 0 1 4 2 Population based output files CDPOP user manual 19 In addition a output csv is automatically created for each batch and Monte Carlo run These are population based metrics calculated at each E generation The following is a summary of each calculation Year This is the generation time Population The total population in each generation This is always constant right now Demographics and population dynamics is coming soon ToTFemales The total number of females in each generation ToTMales The total number of males in each generation BreedFemales The total number of breeding age females in each generation BreeMales The total number of breeding age females in each generation Emigrants The number of left over offspring at each generation These get deleted from the program and are no longer considered F Immigrants The number of immigrants that came in to fill up a habitat location or a grid location ro Births The number o offspring born at that generation Deaths The number
20. inal les the maximum dispersal distance in The user cost units an individual heterosexual but individuals mate unction choice heterosexual r or no females emales have mated that is a bounded ra E E distribution number the user Mendelian inh F in With hermaphroditic mating The probability is one at no distance location and goes to zero at the maximum dispersal ed by the user as either hermaphroditic or exch eproduction and th E B E a Poisson draw with speci there are no distinct sexes with other individuals according to the movement anging genes in Mendelian reproduction mated pairs are one male to possibly many e end of the mating process occurs when all ach mated pair can have a number of offspring dom draw based on a uniform probability In ied mean eritance with k allele mutation or a constant rate chosen by is used to generate the offspring s genotype and the sex assignment is random CDPOP user manual 5 Dispersal of offspring occurs from the mother s x y location according to the selected movement function and the sex of the individual The vital rates birth and death define whether or not the population will have emigrants or immigrants Simulating natural selection Past versions of CDPOP modeled three sources of genetic variation gene flow genetic drift and mutation These versions assu
21. ion a unique identifier for each individual corresponding to a unique subpopulation XCOORD x coordinate location YCOORD y coordinate location YCOORD 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 with a header file Age Structure Filename The distribution that is used to initialize each individuals age If N is entered then this file is not used If a filename is ntered 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 a row of age classes number of individuals observed in that age class and then the proportion of individuals in CDPOP user manual 11 that age class Mate CD Matrix Filename ED cdmatrix16 A nxn 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 See the example 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 A nxn cost distance matrix for dispersal mov
22. ividual can search for a mate You can specify max to consider all individuals for mating movement You can also Mate place an integer value in front of max to Movement 5 consider a percent cost distance movement for Threshold 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 If you want females to mate with replacement Female Y e i B placement N then specify Y you want females to mate p without replacement then specify N If you want males to mate with replacement Male ay Mv lA TE Basis coment Y then specify Y you want males to mate Re without replacement then specify N If you want to allowing selfing i e Selfing N individuals mate with themselves then Answer specify Y If you do not want to allow for selfing then specify N Y for sexual reproduction and N for asexual reproduction With asexual reproduction all n individuals mate and bear offspring with mates selected according to Repro the movement function choice and without duction Y regard to any gender or mating type It is Answer important to note that this asexual reproduction is functionally the sexual paring of hermaphroditic asexual in th distinct sexe e se s b individuals thus it is nse that there are no ut is sexual i
23. med that different genotypes have an equal probability of surviving and passing on their alleles to future generations and thus natural selection was not operating CDPOP V 1 0 implements natural selection analogously to the adaptive or fitness landscape of allele frequencies Wright 1932 This new functionality nables extension of landscape genetic analyses to explicitly investigate the links between gene flow and selection in complex landscapes at an individual s level The user specifies fitness landscape surfaces for each genotype of a single diallelic locus that E is under selection For example three relative fitness surfaces must be specified for the three genotypes AA Aa and aa from the two alleles A and a Selection is implemented through differential survival of dispersing individuals as a function of the relative fitness at the location on that surface where the dispersing individual settles CDPOP v1 0 reads and extracts genotype and location specific fitness values for each n x y individual in the pre processing step The program will continue all other processes the same as CDPOP with an additional step implement selection during 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 manager
24. n the sense CDPOP user manual 13 that individuals mate with other individuals exchanging genes in Mendelian reproduction In sexual reproduction mated pairs consider male and females with or without replacement Repro duction Age The age at which individuals can start to reproduce Use with overlapping generations i e oldmortperc not set to 100 This value must be 0 if you are using nonoverlapping generations 3 4 Dispersal parameters Here lists the parameters used for the movement of individuals with regards to offspring dispersal File Header Example Description Female This is the function answer for movement for Dispersal 2 female dispersal 1 Linear 2 Inverse Movement Square 3 Nearest Neighbor 4 Random Number Mixing and 5 Negative Exponetial Female Dispersal 1 Used only for negativ xponential y a 10 ovement bx and is the parameter a parA Female Dispersal 2 Used only for negativ xponential y a 10 Movement bx and is the parameter b parB A threshold option in cost distance units for how far an individual female offspring can disperse You can specify max to consider all individuals for mating movement You can Female i a i also place an integer value in front of max Dispersal i i 5 to consider a percent cost distan
25. of deaths of the adult population not the offspring Alleles This is the total number of unique alleles at each generation This value can 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 alleles in the population and subpopulation values follow after He This is th xpected heterozygosity value at each generation This value can 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 He in the population and subpopulation values follow after Ho This is the observed heterozygosity value at each generation This value can 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 MateDistCD Th
26. r each column header and the parameters that can be changed Start the program with a graphical interface s section 2 3 2 or at the command line as follows If you use python from the command line then open a terminal window and change your shell directory to the CDPOP home directory Run the program There are a number of ways to run this program If you are using a command shell you can run the program by typing python CDPOP py inputvariables csv Note that the program CDPOP is called followed by a system argument which is the name of the input variable f F ile that you specify with extensions 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 batchrunOmcrun0O batchrunimcrun0 and batchrunimcrunl will be created in your CDPOP home directory to store output from the separate batch and or Monte Carlo runs Each of these folders will have a unique date time stamp preceding batchrunOmcrun0 in case you want to run multiple CDPOP runs in this same directory The program will also provide a log file with program steps and timing events in your CDPOP home directory cdpop log 2 3 2 GUI Run The following are instructions for a simulation run with an optional graphical user interfac GUI
27. re 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 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 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 CDPOP user manual 7 administrati ve 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 will install installer or visitin
28. ription This is the number of offspring each mate pair can have Choose 1 for a random draw 2 Offspring Number 2 for Poisson draw and 3 for a constant number of offspring for each mother or mate pair The parameter value used with Offspring Number If offno 1 then lmbda is the max range value between 0 lmbda to draw Lambda 5 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 Percent number of female born in each 50 i Percent litter i The answer to hav very generation start Equal Sex a Ratio Y wath equal sex ratios Possible options include N and Y OTB g Percent mortality in the offspring Mortality 0 opel cio Percent 3 6 Genetic parameters The following lists the parameters associated with the initialization of the genotypes mutation rates and mtDNA option File Header Example Description Gene Swap 0 The generation time that genetic information Generation starts to be exchanged En 0 0005 The k allele model mutation rate Rate Loci 10 The number of loci The choice for how to initialize the genotype for each n x y individuals If Intialize random is entered then the genotypes get Genes random a random assignment and the population is at Answer a maximum genetic diversity If file is entered then the genetics get drawn from the all
29. s Current needs include quantitative and spatially explicit predictions of current and potential future patterns of fragmentation under a range of climate change scenarios Opdam amp Wascher 2003 To address this need CDPOP v1 0 allows users to input a new landscape surface at a given generation time through new cost distance matrices for both mating and dispersal The program is written in Python 2 6 and provided with installation instructions for most platforms along with sample input files CDPOP v1 0 is built on a driver module plug in docking architecture that F allows for ease of future modular development CDPOP v1 0 has been debugged as carefully as possible by testing all combinations of simulation options Information for users including user manual FAO publications ongoing research developer involvement and downloads can be found at http cel dbs umt edu software CDPOP 2 Getting started 2 1 Dependencies 2 1 1 Baseline Requirements CDPOP requires the Python2 6 x interpreter NumPy package and SciPy CDPOP user manual 6 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 Py
30. spatially explict cost distance populatin genetics program Molecular Ecology Resources 10 156 161 Version X 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 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 abou
31. t al 2010a Landguth et al 2010b Cushman and Landguth 2010 Example simu lations have included 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 1 3 How does CDPOP work CDPOP v1 0 models genetic x y located individuals as fun movement through mating and dispersal user must speci interface or input script file n processes genetic structure across many runs mos CDPOP user manual 4 VvV ctions of ital i F As the m y the input parameters through a odel xchange for a given resistance surface and ndividual based dynamics and mutation graphical user ulates stochastic J A sim t applications will quantify mean and variability of Thus provided for the user to choose the n single set o frequently wish to launch several F simultaneously provided through batch capability In addit run sensitivity analys input parameters UA lA ion is The simulation program assumes constant popul Individual Pad rom a fil reading in a a Monte Carlo option is umber of ru ns to simulate given a a user may also s with different parameter values This functionality is lation density over time s are assumed to occupy a fixed grid on the lan
32. t the program at all times We will welcome questions about how to run CDPOP or interpret the output only after you have read the CDPOP user manual 21 entire documentation This is only fair and will eliminate many trivi al questions Finally we are always interested in learning about how 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 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 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
33. thon 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 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 a
34. vidual based output files The following is a list o options to calculate cost matrix F genetic distance matrices output options from CDPOP distance matrices a and genotype formatting including Euclidean distance File Header Example Description EDmatans N This is the answer If matrix used locations ayer gt is cal idean distance matrix then the Euclidean distance the n original grid culated If N is entered Eucl for will be call then this matrix is not created This matrix ed th EDmatrix csv and outputted in batch and Monte Carlo folder respectiv GDmatans This is the genetic distance matrix The genetic distance matrix used for answer the n a original generatio calculated proportion Curtis distance measure grid locations for specified n time of the simulation run is Enter braycurtis for the Bray Dps for the of shared alleles or Da for Dps longest to total C Nei s genetic distance you do not want to calculate these matrices Note that Nei s genetic distance takes the slightly expensive in computation time and we are working on speeding these up Specify N here if calculate and may decrease your DPOP simulation time All are Gridformat General E will This is the genotype output format option The format for t
35. vo aaBB aaBB mortality fitness surface is used When CDEVOLVE Answer is 2 then this is the Fitness Fitvals0 offspring viability selection surface for AABb AABb If offspring has AABb then this mortality fitness surface is used When CDEVOLVE Answer is 2 then this is the Fitness Fitvals0 offspring viability selection surface for AaBb AaBb If offspring has AaBb then this mortality fitness surface is used When CDEVOLVE Answer is 2 then this is the Fitness Fitvals0 offspring viability selection surface for aaBb aaBb If offspring has aaBb then this mortality fitness surface is used When CDEVOLVE Answer is 2 then this is the Fitness Fitvals0 offspring viability selection surface for AAbb AAbb If offspring has AAbb then this mortality fitness surface is used When CDEVOLVE Answer is 2 then this is the Fitness Fitvals0 offspring viability selection surface for Aabb Aabb If offspring has Aabb then this mortality fitness surface is used CDPOP user manual 17 Fitness aabb Fitvals0 When CDEVOLVE Answer is 2 then this is the offspring viability selection surface for aabb If offspring has aabb then this mortality fitness surface is used 3 8 CDINFECT These parameters are
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