CDFISH user manual - Computational Ecology Laboratory
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1. CDFISH user manual 17 Fitness Aa Fitvals50 txt When CD G G VOLVE Answer is 1 th en this is the offspri sel Aa If g viability lection surface for offspring has Aa the mortal surface Uniform this lity fitness is used selection surface S 0 5 Fitness a a FitvalsNO S100 txt G When CD VOLVE Answer Py is 1 th offspri en this is the g viability THe aa selection surface for offspring has aa the surface Gradie this mortality fitness is used t surface selected for in the north with completely lethal in the Sorth 4 Output The following is a list of the output produced from CDFISH Example Description Grid0 csv generations The genotype for each n x y across specified Output csv lation Dispers Popul Strayers Males al Deaths Deaths Births Adult Deaths Mutated Migrants Offspring Deaths Alleles He A file of the various data measures at each generation Females Residors Selection H Alleles Folders will be created in your project directory label unique tin dos convention Monte Car ne stamp o runs will be uniquel batch run folder yo individua status TE e d with a o will ed bat2. 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 class This number must sum to the carrying capacity of your study or the total number of xy vo location specified above CostDistance Matrix Cdfish test cd The cost distance matrix from source to each subpopulation Note that if you have 4 subpopulations then this file will be a 5x5 matrix The first entry in this matrix is considered the source and these values are used in the migration process The rest of the values are used for the straying process Use a cd extension and comma delimited values 3 2 The following Model parameters lists the model parameters used for CDFISH File Header Example Description 1 replicate The repeated number of simulations to peu pS GOO OAN be conducted for the Monte Carlo method onte Carlo folders labeled E i x p i e the number of replicates for 1 Replicates with mcrun0 y batch of parameters merunl Looptime Simulation run time generation or Genera
3. Burningen This is the generation or year that the selection surface will in previous field specified for is ignored the locus or loci under selection cdevolveans cdevolveans begin operating on specified If N is then this field 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 offspring mortality percentage That value then becomes the individual 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 with 6 lines of header information and values that are formatted files space delimited fitvals txt for for uniform and gradient and represent percent mortality 0 100 an example fitness surface and its format spatial selection files These are ASCII See Examples are given Fitness AA FitvalsN100 SO txt When CDEVOLVE Answer is 1 then this is the offspring viability selection surface for AA If offspring has AA then this mortality fitness surface is used Gradient surface selected for in the south with completely lethal in the North ry
4. 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 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 A good suggestion for all in one installations is through the superpack Windows 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
5. 1 Install Python and NumPy Make sure that Python and NumPy are installed and available to you You can test this by typing python at a command window If python is available you ll get the python prompt gt gt gt If it is not a recognized 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 If python does not complain that there are no such modules all is CDFISH user manual 7 well The following instructions assume Python and NumPy are not yet available on your computer 1f they are skip to section 2 2 2 First run the Python executable installer you ve chosen 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 packages in their default locations Next install NumPy using the supplied executable installer This will install NumPy in your Python site packages directory If you downloaded enthought s version y
6. Cushman et 3 nmixia within this cost distance to provide a consistent and comparable framework to evaluate the pattern process relationships resulting from iso ation by resistan distance and isola Demographics within tion by barriers subpopulations ce isolation Cushman and by Euclidean Landguth 2010 Individuals are assumed to occupy subpopulations on the landscape that is user defined by the x y locations vital dynamics subpopulation its original genotype of each lo 1 e maximum alle cus for each is ini lation numbers th offspring straying to another offspring to make it n resistance The simulation program assumes a carrying capacity within each subpopulation and allows for varying popul birth and death rates and or the inability of an subpopulation due to a high strean individual rough back to The lic diversity population and the sex of each initial Reproduction is heterosexual with a random pairs can be chosen replacement Poisson draw with s inheritance with k The initial individual tialized randomly age structure of the is user defined based on male or E emale with mating structure Mated or without Each mated pair can have a n bounded random draw based on a uniform probability distribution umber of offspring th a
7. in each generation you specify subpopulations in the first column of your xy csv file then this field will be separated by The first value is the total male size and each additional value corresponds to the subpopulation sizes in order Migrants The number of dispersers in each generation that make it to the next generation Residors The number of residents in each generation that make it to the next generation Strayers The number of strayers in each generation that make it to the next generation DisperseDeaths The number of dispersers in each generation that do not make it to the next generation Death due to a weighted random draw from probability based on functional cost distance choice Or the number of individuals that could not disperse migrate or stray due to high cost to moving to an open locations Offspring Deaths The individuals left over from dispersal process discarded Selection Deaths Individuals that made it back to population but did not survive do to differential mortality of genotype and spatial selection Births The number of offspring born at that generation Adult Deaths The number of deaths of the adult population not the offspring born that year generation The separates th age class deaths for overlapping generations for the ordered ag class in that generation Note that some years may not have all age c
8. 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 CDFISH This program was developed by Erin Landguth and Clint Muhlfeld The reference to cite is Landguth EL Muhlfeld CC Luikart G 2012 CDFISH an individual based spatially explicit landscape genetics simulator for aquatic species in complex riverscapes Conservation Genetics Resources 4 133 136 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 CDFISH 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 Although this program has been used by the USGS no warranty ex pressed or implied is made b
9. with sample input files CDFISH v0 5 is built on a driver module plug in docking architecture that allows for ease of future modular development CDFISH has been debugged as carefully as possible by testing all combinations of simulation options Information for users including this user manual FAQ publications ongoing research developer involvement and downloads can be found at http cel dbs umt edu software CDFISH rat 1 1 Changes from CDPOP v1 0 There are major innovations in CDFISH which were not included in CDPOP We list below the new functionalities of CDFISH e Subpopulations of individuals Individual x y locations can now be grouped into subpopulations on the landscape that could represent home spawning grounds for example e Population dynamics Subpopulation numbers can now fluctuate as a function of vital dynamics straying and or the inability of an individual to make it back to its original subpopulation e Offspring have 4 states residency migration straying or death With residency offspring do not disperse back to the source location lake or ocean for example but reside in their original subpopulation Migration is a probability of returning back to a subpopulation that is a function of the stream resistance surface in units of cost If an offspring does not migrate back to its original subpopulation than it can
10. CDFISH user manual 1 CDFISH USER MANUAL 2012 Version 0 55 Last Updated 2013 10 08 Authors Erin L Landguth Clint C Muhlfeld and Gordon 3 Luikart 1 University of Montana Division of Biological Sciences Missoula MT 59812 USA 2 U S Geological Survey Northern Rocky Mountain Science Center Glacier National Park West Glacier MT 59936 USA 3 Univeristy of Montana Flathead Lake Biological Station Division of Biological Sciences University of Montana Polson MT 59860 USA CDFISH user manual 2 Table of Contents T AMELOQUELTLON Sh AA ARA AAA A AAA eet a a 3 lst Changes Trom EDPOB ta a a a Seas eee 3 127 What Can CDETSH Oia jad ae wie eye dd da a ares 3 1 3 How does CDE LPS AM WO Kit A Sa ae A A aS GG aes 3 2 Getting started this dw a ecg i ae Bs esd Wa aw ede NIA A ald oe oe Bee ad 5 251 DEPENGENCLES ed ole Sie Ge eles WE Ores E ack Sie Soa ee ae ele oe 5 2 1 1 Baseline requirementS o oooooooooooo ee eee eee 5 2 122 Python ON NON WINdOWS PTAE FORMS es sj dla a es 5 2 4 53 PY THOM On WINGOWS ir sodas ocd te a Ad ond id See Sake 6 Zi cAsObt ai nang NUMPY et edie cde so baie A ES Gee Sw ERIS oe 6 DSZ PAS CALVaACVON Ge ond ee tl hae ie oe tadd ea Viale ls Gh Mayas ere te 6 Lidl tastes bing Pyehon van Gs NUM sic cence rhe See es a ds os 6 Zi Za 2 Insta
11. ashares JS 2007 Journal of Applied Ecology 44 714 724 Holderegger R Wagner HH 2006 A brief guide to Landscape Genetics Landscape Ecology 21 793 796 CDFISH user manual 21 Landguth EL Cushman SA 2010 CDPOP A spatially explicit cost distance population genetics program Molecular Ecology Resources 10 156 161 Landguth EL et al 2010a Quantifying the lag time to detect barriers in landscape genetics Molecular Ecology 19 4179 4191 Landguth EL et al 2010b Relationships between migration rates and landscape resistance assessed using individual based simulations Molecular Ecology Resources 10 854 862 T Landguth EL Hand BK Glassy JM Cushman SA 2011 UNICOR A species connectivity and corridor network simulator Ecography Submitted McRae BH Beier P 2007 Circuit theory predicts gene flow in plant and animal populations Proceedings of the National Academy of Science USA 104 19885 19890 Parmesan C 2006 Ecological and evolutionary responses to recent climate change Annual Review of Ecological Systems 37 637 669 Parmesan C Yohe G 2003 A globally coherent fingerprint of climate change impacts across natural systems Nature 421 37 42 Ray N 2005 PATHMATRIX a GIS tool to compute effective distances among samples Molecular Ecology Notes 5 177 180 Root TL Price JT Hal
12. ation These versions assumed that different genotypes have an equal probability of surviving and passing on their alleles to future generations and thus natural selection was not operating CDFISH V 0 55 and greater implements natural selection analogously to the adaptive or fitness landscape of allele frequencies Wright 1932 This new functionality enables 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 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 CDFISH 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 above with an additional step implementing selection during the dispersal process ee E CDFISH Input A user must specify the input parameters through an input script file or a graphical user interface GUI As
13. chrun0 be uniquely label u wil l s genotype spatial you specified a grid additiona In additi Monte Car generatio Lly see the format fol on age format option an output csv is automatically created LO run n These are popul lation based metrics The following is a summary o E 133296429 7batchrunOn y labeled mcrun0O mcrunl batchrunl A sex and ncrun r and each In each ll see grid generation csv files that list each locations e infection then you will lowed by grid generation csv F or generations Population The total population in each generation each batch and calculated at each each calculation Year This is the generation time or year if using overlapping If you specify subpopulations in the first column of your xy csv file then this field will be separated by Miles The first val lue is the CDFISH user manual 18 total population size and each additional value corresponds to the subpopulation sizes in order ToTFemales The total number of females in each generation If you specify subpopulations in the first column of your xy csv file then this field will be separated by The first value is the total female size and each additional value corresponds to the subpopulation sizes in order TE ToTMales The total number of males
14. e e masas replacement then specify Y Male Replacement TIEN See Sete pe you want males to mate without replacement then specify N Reproage Me Ss The age at which individuals can start Reproduction individuals to reproduce Use with overlapping Age start generations i e agemortperc not set reproducing at to 100 If an age distribution file is age 0 not used then age gets initialized with 0 at the starting generation 3 4 Dispersal Migration parameters Here lists the parameters used for the movement of individuals with regards to offspring dispersal and migration File Header Example Description This is the function answer for movement for female dispersal probability Linear 1 1 Threshold Cost Distance 2 Inverse Square 1 Cost Distance 2 1 VA 3 Nearest Neighbor Use threshold to specify inverse Moore neighborhood Dispmoveno square Dispersal probability 4 Random Mixing Does not consider dispersal Movement function cost distance matrix Choice for cost distance 5 Negative Exponential parA 10 parB movement Cost Distance 6 Min max scaled 1 min Cost Distance max Cost Distance Cost Distance min Cost Distance 1 where min and max are the minimum and maximum cost distance values in the given matrix CDFISH user manual 13 7 User defined min max scaled Distance max Cos
15. e then open a terminal window and change your shell directory to the CDFISH src home directory i e gt cd C homedirectorylocation src 5 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 CDFISH py C homedirectorylocation data cdfish_test 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 run gt CDFISH py runs CDFISH 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 cfish test csv is the parameter file Note you can always rename this file just make sure you specify the right name in the argument list gt argument 6 Check for succe step by step ou simulation time CDFISH user manual 9 output_test is the name of the directory that will be created with CDFISH output in the directory specified by the th above ird This also can be named whatever you want ssful tput will model run completion The program will in the Shell
16. either stray to another subpopulation at some probability or die 1 2 What can CDFISH do CDFISH 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 aquatic species Example simulations might include e How will changing stream resistant surfaces affect the genetic structure from an individual based setting e What combinations of probabilities of straying migration resi dency and vital dynamics prevent a subpopulation from becoming extinct e How will the incorporation of a partial barrier on the stream r Sistant landscape affect the genetic structure and population dy namics of individuals or populations 1 3 How does CDFISH work Individual based si mulations in rive CDFISH user manual 4 exchange rscapes CDFISH models genetic or a given stream resistance surface and n x y located individuals as functions of individual based movement through mating vita 1 and dispersal pixel represents are given weights o dynamics F the unit cost o r resistance val and mutation users must create a stream resistance surfac Pri wh or to running CDFISH ach cell value crossing each location reflecting the presumed ues P
17. enetic diversity If file is entered then the genetics get drawn from the allele frequency distribution fi specify file name in next column ile all reqfilename F TF N known is entered then the genotypes are directly read from a given known file This file is very similar to the initial xyfilename and example cdfish test _known csv is supplied with test data files CDFISH user manual 16 N allele frequency file not used Allefreq filename locus individual s genotype frequency distribution e or each The allele frequency distribution used to initialize the model s n If you want to use a file you must set Initial then enter in the See allel formatting this file F ize Genes Answer to equal ilename efrequency csv examp It file and field e for ia in this e fil is basical column of allele freq the length of starting loci sure you include th the column equals your starting alleles fil ncies and make sure Al xtension so make allelefrequency csv e g cdevolveans SN This is the answer for under selection Nf Use to turn off CD how many loci are EVOLVE Use 1 for natural se lection with 1 locus 2 or more not coded in yet 10
18. idual corresponding to a unique subpopulation This is an optional tracker for individuals that may be located in designated subpopulations If individuals are just fish test NAs gives you an P cify your starting Xyfilename Thi population size continuously distributed then fill with arbitrary value like 1 If f used then s example is these field is 64 possible habitat locations that can be filled with onl 47 initialized with individuals You must specify NA values in the ID and sex y columns but subpopulations e g 1 2 3 XCOORD x coordinate locatio YCOORD y coordinate location YU YCOORD must be in seg ID a string label identifi r and CDFISH user manual 10 still provide th xy locations that are OPEN and a Supopulation identifier field 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 agedistributi on N no age distribution file The distribution that is used to initialize each individuals age is used and age is initialized at O for all indidivuals NE initialized no file is not used and age with 0
19. ixels influence of each variable to movement or connectivity of the species in al question 2010 e g Dunning et al 19 92 Cushman et al Stream resistance surfaces can be parameterized to reflect 2006 Spear et different costs to movement associated with water temperature and 4 ow habitat compl features From her costs that can be c exity barriers elevation e omp F Ju ndividuals or between all pairs o to calculating cost Dijkstra s algorith program McRae ArcGIS between nd ESR Beier 20 COEP a s such as UNICO distance matrice Dijkstra 1959 R Landguth et 07 PATHMATRIX Redlands CA m individuals with ecological cost distanc slope CDFISH requires as input a matrix o uted based on shortest cost paths algorithms populations or other stream F f movement Common approaches s in landscape genetics include uds al Ray 2005 an By comparing submitted implemented through G CIRCUITSCAPE d COSTDISTANCE in genetic distances researchers can test specific hypotheses about th stream features and environmental co al 2006 Epps eta absolute or partial modeling framework Ts 2007 Jas barriers and pa This is critical nditions on gene The program can flexibly incorporate s between them e influences of ow
20. l KR Schneider SH Rosenzweig C Pounds JA 2003 Fingerprints of global warming on wild animals and plants Nature 421 57 60 Spear S Balkenhol N Fortin M J McRae B Scribner K 2010 Use of resistance surfaces for landscape genetic studies Considerations for parameterization and analysis Molecular Ecology 19 3576 3591 Storfer A Murphy MA Spear SF Holderegger R Waits LP 2010 Landscape genetics where are we now Molecular Ecology 19 3496 3514 Walther G R Post E Convey P Menzel A Parmesan C Beebee TJC Fromentin J M Hoegh Guldberg O Bairlein F 2002 Ecological responses to recent climate change Nature 416 389 395 7 Acknowledgements We are grateful to Leslie Jones and Helen Neville for their valuable input in the model development We thank the numerous beta testers Funding was provided by the Great Northern Landscape Conservation Co operative U S Department of Interior through the Rocky Mountain Co operative Ecosystem Study Unit at the University of Montana Missoula
21. l sex ratios CAREFUL this parameter is not realistic for non panmictic populations and should only be used to match Wright Fisher assumptions on Equalsex equal sex ratios ratio Equal Sex yt AtBirth This will ensure that each Ratio for litter is equal sex ratio but not necessary Offspring 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 3 6 Genetic parameters The following lists the parameters associated with the initialization of the genotypes mutatio n rates and selection File Header Example Description Muterate 10 0005 The k allele model mutation rate Loci vio The number of loci Alleles 107 The number of alleles per locus If you want a variable initial number of alleles per locus then separate the numbers with a e g 2 3 8 3 but make sure that you enter in the total loci amount else an error will be thrown Intialize Genes Answer random 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 g
22. lasses and not reported 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 CDFISH user manual 19 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 e Mutations The total number of mutations at each generation 5 General issues 5 1 How to obtain CDFISH The program is freeware and can be downloaded at http cel dbs umt edu software CDFISH with information for users including manual instructions FAQ publications ongoing
23. ldang CDETSH td ted aa od ees de eld Nee dks 6 22 3 Description OF CDFLSH FILES eee aie 4 oka 7 2 3 ae PUT ove ale tate a elie as A eh ee a ee 7 Sal Command Vane esd oe A A eA ads 7 SZ GUT PUMA ead tae de bei a See eee Stow eh Seed aia 8 Sty MPU ease ES O AN DS ee Bel IO E eval os eee eel E 9 Back POPU PILES ts e bdo ne See et ee eh Ba a we ee Uh es 9 322 Model Parameters dris odie eke Wie Die ee Ee a de Sar eB 10 343 Mating Paramekers lt 9 oie dada da ads 10 3 4 Dispersal Parameters cece sd sad we ah SE da 11 32450 AOEESPEINO Parameters oa a aa sado dy dadas 11 30 GENeCEICG Parameters ise ewan a A O shes 12 A OQUEDUES Sts Swett ee dame a eee ae ae Sie y Sis da eee bet ee 12 5 General US SUES LAA Ca e A ar oe tae OS E A 12 DL Howto Obtain CDFISH cms a a ee a ca dios 12 52 Debugging and troubleshootan Ginna wee esterne ea i enteran 12 4 3 HOW to ette CDS His press ive wl ace aia ie oh ice ang ee sh Sites 12 5 4 Das S C Pa VIMY a a a Sew wth des Bd a ee Ss aa ahs A Gel Bee ers 13 6 Referentes din ee ee wi a esi ee ae A Ii day ws BO gl A ii 13 T ACkNOwLedgement Si eer asie bard oi Seeger ies Saree a bs oe ore veins eines Be aes ey ented a ers ei See l CDFISH user manual 3 1 Introduction The goal of this user manual is to explain the technical aspects of the current release of the CDFISH program v0 5 The program is written in Python 2 7 and provided with installation instructions for most platforms along
24. n file gt allelefrequency csv example allele frequency distribution file F CDFISH user manual 8 gt cdfish test csv run parameters corresponding to the example files 2 3 Example run 2 3 1 Command line run The example run is for 64 points 4 subpopulations with 16 individuals in each representing individuals with an example cost distance matrix 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 cdfish test csv specifies the parameters that can be changed and used in a sample CDFISH run Open cdfish test csv in your editor of choice A spreadsheet program like Microsoft Excel F allows for easy editing of the tabular values 3 There will be 3 lines of information in cdfish test csv a header line and 2 lines of information corresponding to 2 separate CDFISH 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 listed is for the 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 4 Start the program with a command line For example if you use python from the command lin
25. ou will not need to install a separate NumPy installer 2 2 2 Installing CDFISH for Linux or Windows Next install the CDPOP software itself by unpacking the zip archive supplied Navigate to the directory on your PC where you wish to install CDFISH and unpack the supplied zip archive file using a free archive tool like Zip 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 supplied test inputs 2 2 3 Description of CDFISH files 3 directories will be installed in your directory Here is a description of each 1 src CDFISH source code Li AOC gt gt README txt a quick how to run CDFISH instructions gt CDFISH user manual pdf this file gt CDFISH history txt Notes on history and version changes 3 data Example input files gt cdfish test cd example cost distance matrix file Here 5x5 Source and each population cost with cost between populations gt cdfish test xy example n x y file for individuals gt cdfish test NAs csv example n x y file with sparse individuals gt agedistribution csv example age distributio
26. rd to hearing about your applications 6 References Allendorf FW Luikart G 2007 Conservation and the genetics of populations Blackwell Malden MA Balkenhol N Gugerli F Cushman SA Waits LP Coulon A Arntzen JW Holderegger R Wagner HH 2009 Identifying future research needs in F landscape genetics where to from here Landscape Ecology 24 455 463 Balkenhol N Landguth EL 2011 Simulation modeling in landscape genetics on the need to go futher Molecular Ecology 20 667 670 Cushman SA McKelvey KS Hayden J Schwarz MK 2006 Gene flow in complex landscapes testing multiple hypotheses with casual modeling The American Naturalist 168 486 499 Cushman SA Landguth EL 2010 Spurious correlations and inferences in landscape genetics Molecular Ecology 19 3592 3602 Dijkstra EW 1959 A note on two problems in connexion with graphs Numerische Mathematik 1 269 271 Dunning JB Danielson BJ Pulliam HR 1992 Ecological processes that affect populations in complex landscapes OIKOS 65 169 175 Epperson BK Mcrae BH Scribner K Cushman SA Rosenberg MS Fortin MJ James PMA Murphy M Manel S Legendre P Dale MRT 2010 Utility of computer simulations in landscape genetics Molecular Ecology 19 3549 3564 Optimizing dispersal and corridor models using landscape genetics Epps CW Wehausen JD Bleich VC Torres SG Br
27. ssignment from percent 50 random given percentage i e even if you set this Female female to 50 some generations could have 499 offspring assignment female births and 501 male births for example birthmortpe 0 0 Percent mortality in the offspring re birth population mortality Agemortperc 100 Age This is the mortality field for each age Age structured class Each age class must be separated with Structure mortality er e Mortality here with non overlapping generations then specify numbers which is the same as this situation adu and adult t mortality is set to If looking at non overlapping generations offspring mortality the birth mortality in mortality where 1005 If looking at overlapping generations with a ass e g age classes 0 1 2 3 supplied age distribution cl 4 then a mortality F percentage must be 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 Al age classes beyond specified in E ile will get lumped into last mortality category CDFISH user manual 15 This ensures an exact equal sex ratio for the following options WrightFisher The answer to have every generation start with equa
28. stance 2 1 4 random Matemoveno aa 3 Nearest Neighbor Use threshold to probability i Mating specify Moore neighborhood function of Movement mating cost Function ang 4 Random Mixing Does not consider distance cost distance matrix 5 Negative Exponential parA 10 parB Cost Distance 6 Panmictic Window Given the cost distance matrix then movement will be panmictic within set movement threshold A threshold option in cost distance Matemove i pS i ar y thresh units for how far an individual can Matin v57 search for a mate equivalent to the g cost distance kernel You can specify Movement p gt a fea E max to consider all individuals for Threshold f F mating movement You can also place an CDFISH user manual 12 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 f you want females to mate with Freplace N females replacement then specify Y Female mate without Replacement replacement f you want females to mate without replacement then specify N f you want males to mate with Mreplac
29. t Distance Cost Distance min Cost Distance 1 where min and max are the minimum and maximum cost distance values specified by the dispmovethresh option 1 min Cost A threshold option in cost distance units for how far an individual male offspring can max disperse You can specify max to consider will travel all individuals for mating movement You can the entire also place an integer value in front of max Diapmoves landscape to consider a percent cost distance movement thresh as an for mating For example 10max would consider pispe rsal inverse all mating individuals that are within 10 M ven nt square percent of the maximum cost distance on the Threshold probability surface You can also just specify a specific of cost cost distance value distance on the If dispermoveno option 7 is used then two surface values must be specified for the minimum and maximum threshold values and separated by a V7 This is the percent of the subpopulation s 10 10 10 1 open locations that take up residency Eram the Residency 0 offspring pool There needs to be a unique value for each subpopulation separated by a WARA This is the percent for each subpopulation for the offspring that do not make it back to Staviti 10 10 10 1 their own subpopulation that stray to another 0 subpopula
30. t isa E pecified mean allele mutation a A or a constant number Mendelian rate chosen by the user is used to generate the offspring s genotype and the sex assignment is random Dispersal through residency strayin ither reside in a ch subpopulation g e g and migration stream or tributary Offspring can or CDFISH user manual 5 disperse to a source location e g lake river or ocean Offspring that disperse to the source must migrate back to their respective subpopulation or stray to another subpopulation Straying and residency probabilities are user defined for each subpopulation Migration to subpopulations is a linear function of the stream resistant riverscape Individual offspring move a distance from their source location based on a random draw from a probability distribution inversely proportional to a linear function probabilities range from one at no distance from the original location to zero at the maximum dispersal distance To realistically reflect species specific dispersal abilities the user specifies the maximum dispersal distance in cost units an individual can travel expressed as the maximum path length for a species given its dispersal ability Simulating natural selection Past versions of CDFISH modeled three sources of genetic variation gene flow genetic drift and mut
31. the model simulates stochastic processes most applications will quantify mean and variability of genetic structure across many runs Thus a Monte Carlo option is provided for the user to choose the number of runs to F simulate given a single set of input parameters In addition a user may also frequently wish to launch several runs with different parameter values simultaneously i e sensitivity analysis This functionality is provided through batch capability See Section 3 for program input details CDFISH Output There are two model outputs The first is a series of coma delimited files specifying the locations genotypes age and sex of each individual at specified simulation years The second output is a file containing yearly values for various population parameters formatted to facilitate graphical display See Section 4 for program CDFISH user manual 6 output details 2 Getting started 2 1 Dependencies 2 1 1 Baseline Requirements CDFISH requires the Python2 7 x interpreter and NumPy 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
32. tion There needs to be a unique value for each subpopulation separated by a Yea 3 5 Offspring parameters The following lists the parameters to deal with offspring births and deaths File Header Example Description This is the number of offspring each mate pair can have 1 for a random draw a E Poisson 2 for Poisson draw Choice distributio n 3 for a constant number of offspring 4 for an equal clutch size for each female CDFISH user manual 14 Note that option 1 3 will assign a clutch size to each mate event males female mates with 4 to 3 with lambda of 2 offspring Option 4 DE j a femal set to 4 with lambda of 2 F have 2 offspring total and the father s For example if a and offno is set then she will have 8 will assign a clutch size to each female that mated For example e mates with 4 males and offno is then she will E is randomly selected from the 4 mating events The parameter value used with Offspring Number 5 If offno 1 then lmbda is the max range value between 0 lmbda to draw randomly Poisson A Lmbda distributio 29 o EF offno 2 then lmbda is the Poisson mean lambda 5 az for the litter size If offno 3 then lmbda is the constant litter size value Percent number of female born in each Female OT a litter This is a random a
33. tion Ti pf year File output indexed from 0 me looptime 1 For Nthfile Sequence The choice of a specified simulation Choice will save a run time to write to file If List is Generations specified entered then read nthfile list values CDFISH user manual 11 of Saved sequence of below If Sequence is entered then Genotypes generations read nthfile seq value below Choice Nthfile The POTER simulation run time to List List write to fi e and to calculate genetic of 101314 distance matrices These values are used if nthfile choice List These Generations a A values must be separated with a Saved vertical bar The specified simulation run time to write to file and to calculate genetic Nthfile distance matrices This value is used Sequence if nthfile choice Sequence This is Sequence of xI the by value in the sequence For Generations example would create values starting Saved at 0 ending at looptime 1 by every 1 generation A value of 5 would output every en generation etc 3 3 Mating parameters The following individuals due to mating lists the parameters used for the movement of File Header Example Description Movement function answer for mating probabililty 1 Linear 1 1 Threshold Cost Distance 2 Inverse Square 1 Cost Di
34. window Once completed a provide batchrunOmcrunl created in your separate batch the data folder a unique date t CDFISH runs in be printed out and folders batchrunOmcrun0O batchrunlmcrun0 and batchrunlmcrunl will be CDFISH home directory to store output from the and or Monte Carlo runs These folders are located in specified in above step The output folder will have ime stamp proceeding in case you want to run multiple log file with p this same directory The program will also provide a rogram steps in your specified output directory If parameters are generation time 2 3 2 GUI Run Sorry are less than 0 52 current updates are not supporting the GUI such that population becomes extinct before specified then program will end See versions that for GUI runs tionalities are incl However latest and greatest func uded in versions greater than 0 52 3 Input 3 1 Input files The following are the general input files used in CDFISH See examples provided for formatting your input files File Header Example Description Cdfish _test xy example supplied The n x y grid location values This is a comma delimited file with 5 column cd CSV spe example of how to initial for the 64 headings individuals in 4 subpopulations Subpopulation a unique identifier for each indiv
35. y the USGS or the United States Govern ment as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty and no responsibility is assumed by the USGS in connec tion therewith We strongly urge you to read the entire documentation before ever run ning CDFISH We wish to remind users that we are not in the commer cial software marketing business We are scientists who recognized the need for a tool like CDFISH to assist us in our research on land CDFISH user manual 20 E scape genetic issues Therefore we do not wish to spend a great deal of time consulting on trivial matters concerning the use of CDFISH However we do recognize an obligation to provide some level of infor mation support Of course we welcome and encourage your criticisms and suggestions about the program at all times We will welcome ques tions about how to run CDFISH or interpret the output only after you have read the entire documentation This is only fair and will elimi nate many trivial questions Finally we are always interested in learning about how others have applied CDFISH in ecological investiga tion and management application Therefore w ncourage you to con tact us and describe your application after using CDFISH We hope that CDFISH is of great assistance in your work and we look forwa
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