POPDIST, Version. 1.2.4: User's Guide
Contents
1. POPDIST Option Version of Measure i Use a identity estimating measure if available d Use a distance reconstructing measure if avail able p Use a topology reconstructing measure if avail able Other Functions m Start up with menu j Calculate jackknife of standard error of the esti mate over loci 0 Reuse the files in the previous run as stored in f filename o filename the file oldfiles tlh in the current directory Use files specified in the file given by filename Put out put into the file given by filename instead of to the screen s screenwidth Set width of screen for output to screenwidth char Table 2 Summary of auxiliary functions and variants of measures implemented in POPDIST acters for output Measure Property Topology Distance Identity Polyploid 1983 weighted Reynolds et al 1983 unweighted Cavalli Sforza amp Edw l forza amp Papi Table 3 Summary of the capabilities of the measures implemented in POPDIST version 1 2 4 Topology and distance both indicate measures of genetic distance If both Topology and distance are indicated they are the different recommended forms of the measure for reconstructing tree topology and genetic distances Identity indicates whether the method implements a measure of genetic iden tity Polyploid indicates that the measure is applicable to comparisons involving polyploid populations 1 The polyploid version of Hedrick s Do2. POPDIST Version 1 2 4 User s Guide Bernt Guldbrandtsen J rgen Tomiuk and Volker Loeschcke October 9 2012 Dept of Genetics and Biotechnology University of Aarhus Research Center Foulum PO Box 50 DK 8830 Tjele Denmark Phone 45 89991227 Fax 45 89991300 e mail bg genetics agrsci dk Dept of Anthropology and Human Genetics Wilhelmsstrasse 27 D 4000 T bingen Germany Phone 49 0 7071 297 6883 Fax 49 0 7071 297 5233 e mail juergen tomiuk uni tuebingen de FDept of Genetics and Ecology Aarhus University Ny Munkegade Bldg 540 DK 8000 Aarhus C Denmark Phone 45 8942 3268 Fax 45 86127191 e mail volker loeschcke biology aau dk Contents 1 Introduction 2 Input File 2 1 The Header e 2 2 Data For One Population o o 2 2 1 Missing Values 2 3 Polyploid Populations o o e 3 Running the Program 3 3 1 The File Selection Screen Gog ap itn e 3 3 3 Measure Selection Commands 3 3 4 Measure Variant Selection Commands 3 4 Output e rs aaa RA a is a ln a id E 2 11 12 12 12 13 1 Introduction POPDIST is a program for the calculation of various population genetic distance and identity measures It uses an input file format that is similar to the input format used by the GENEPOP software Raymond amp Rousset 1995 and files creat
3. e would appreciate a copy so that it can be made available on the net 7 Acknowledgements We thank the European Science Foundation for supporting the visit of JT to Aarhus grant no ESF POBI 95Y and the Danish Natural Science Research council for supporting parts of the project grant no 9701412 to VL 12 A Summary of Options filename filename screenwidth g se the measure of 1978 Use the measure of Tomiuk et al unpubl Use the measure of 1971 Use a distance reconstructing measure if available If a distance reconstructing version of the measure is not available the program chooses another measure to calculate se the weighted measure of Reynolds et al 1983 U Use files specified in the file given by filename Use the measure of Use the measure of Hillis 1984 Use a identity estimating measure if available If a identity re constructing version of the measure is not available the program chooses another measure to calculate Calculate jackknife of standard error of the estimate over loci Start up with menu Use the measure of Reuse the files in the previous run as stored in the file oldfiles tlh in the current directory Put out put into the file given by filename instead of to the screen Use a topology reconstructing measure if available If a topology reconstructing version of the measure is not available the program chooses another measure to calculate Set width of screen for outpu
4. ed for GENEPOP for diploid populations are read unmodified by POPDIST 2 Input File The genetic data are entered into the program by reading one or more input files The input file format is an extended version of the input file format for the GENEPOP package The file format is a simple ASCII format Each file is composed of one header and the genetic data for one or more populations The program is executed either through command line options or through a simple menu system It is the first program to implement the genetic distance and identity measures of 11995 for codominant al leles The measure is very robust against non equilibrium conditions and can also be applied to microsatellite data In contrast to alternative measures this measure is able to estimate genetic distances involving polyploid and partheno genetic populations Tomiuk amp Loeschcke 1996 Also the measure of Tomiuk and Loeschcke has recently been shown to have very desirable statistical prop erties Tomiuk et al 1998 The program has run quite fast regardless of which of the available options are included and it is reasonably memory efficient 2 1 The Header The header is composed of one line of comments followed by lines with the designations of the loci one name on each line beginning in column 1 of the lines The first line is discarded by the program while the locus designations are used in the program output The number of loci and their names mus
5. er run 3 2 Choosing Measures and Other Options The options for choosing among the measures are shown in table 1 Most measures come in several modifications often they allow both the esti mation of genetic identity between populations and of genetic distance between populations Some measures have different variants of a distance measure de pending on whether reconstruction of topologies or distances sensu 1996 is desired Additionally there is a number of options modifying the actions of the program These options are shown in table 2 The capabilities of the measures that have been implemented in POPDIST are summarized in table 3 3 3 Using the Menus All the features of the program are also available through a simple keyboard driven menu system On a Macintosh the program automatically launches with the menus Under MS DOS and Unix the menus can be launched in either of two ways Either by just typing popdist at the prompt or by using command line options and including the m option Option Measure Table 1 Summary of options for choosing genetic measures implemented in Use the measure of Use the measure of Nei Use the measure of Hillis 1984 U Jse the weighted measure of Reynolds et al Use the unweighted measure o 1983 se the measure of Edwards se the measure of Hedrick 1971 se the measure of Cavalli Sforza_4 1967 se the measure of default aq
6. f available The s command chooses the distance reconstructing version of a genetic distance measure if available The i command chooses to do estimation of genetic identity This is the default The j command chooses to do jackknife estimation of the standard error The o command chooses not to do jackknife estimation of the standard error This is the default The command This will show a brief summary of the commands The q command Using this command causes the program to exit immedi ately The c command causes the program to calculate genetic measures as cur rently selected 3 4 Output The program returns a matrix of genetic identities or optionally genetic dis tances between the set of populations described in the data file s The program can calculate jackknife of standard error If the jackknife option is used the mean of the individual jackknife estimates is calculated instead of the normal joint estimate across all loci Note however that the last two estimates may be identical depending on the measure chosen The width of the matrix defaults to 80 characters This can be changed with the s option minimum 30 Normally the output is sent to the screen However this can be modified using the o option which can be used to specify an output file 10 3 4 1 Output Values If the j option is not used i e jackknife estimates are not calculated all output values are the values given by the measure in
7. is only in directly supported see text 2 Described by Nei _et_al 1983 and amp Nei 1996 3 The Snes reconstructing measure ae the square root correction Tomiuk et al 1 1998 The menu has two screens one for entering and removing data files from the calculation and one for choosing the measure to be calculated Everything operates by typing one letter commands followed by hitting the return key which be labeled enter depending on your keyboard Depending on the com mand you gave the program may then prompt you for additional data Type in the data and finish by hitting return All commands are case insensitive i e uppercase and lowercase letters do the same thing 3 3 1 The File Selection Screen The File Selection screen consists of three parts e First it lists the names of input files entered up to now I you started the program on a Macintosh or by just typing popdist followed by return it should just say No files here at this point e The second part shows where output will be written The default is to write output to the screen e The third part shows the available commands The available commands are The a command The simplest way to add files is to use the a command You will be prompted for the name of an input file in the current directory Files will be added to the list of data files selected The r command To remove a file from the list of input files u
8. ly chosen second whether Jackknife of the stan dard error of the estimates will be calculated and third what variant of the measure is calculated Notice that many combinations of choices measure and variant are valid See table B for valid combinations e Second there is a listing of the available commands 3 3 3 Measure Selection Commands The t command chooses the measure of Tomiuk amp Loeschcke 1991 This is the default The n command chooses the measure of 1972 The r command chooses the measure of 1972 The e command chooses the weighted version of the measure of Reynolds 1553 The h command chooses the measure of 1984 The g command chooses the measure of 1995 The k command chooses the measure of 1971 The 7 command chooses the measure of 1978 The w command chooses the unweighted version of the measure of Reynolds et al 1353 The a command chooses the chord version of the measure of 1967 Notice that I divide the measure by the number of loci in order to handle cases where comparisons between pairs of populations differ in the number of loci for which data are available for comparison i e when one or both populations in a comparions have no data for one or more loci The b commnand _ chooses the band shareing measure of Tomium et al un publ 3 3 4 Measure Variant Selection Commands The p command chooses the topology reconstructing version of a genetic distance measure i
9. on and one triploid popula tion with the following data in the file exmpl2 dat 11 This is example 2 Enzymel Enzyme2 Pop Examplpop1 0102 0103 Examplpop1 0101 0204 Pop Examplpop2 010101 010103 Examplpop2 010202 020203 Examplpop2 010104 020203 When genetic identities with jackknife estimates of the standard deviations using the Tomiuk amp Loeschcke measure with the command popdist j exmpl2 dat the result should be Tomiuk Loeschcke s Identity estimating measure Examplpop1 Examplpop2 Examplpop1 1 000 0 000 0 901 0 025 Examplpop2 0 901 0 025 1 000 0 000 5 Obtaining the Program The program can be obtained from http genetics agrsci dk bernt popgen Users who do not have access to the World Wide Web may send a MS DOS formatted 1 4 MB disk to the first author The program will be available in precompiled versions for the Macintosh IBM PC compatible computers and various brands of UNIX Availability of UNIX precompiled versions depends on what machines currently are available to us Up to date information about new versions of the program will be available at the web site 6 Bugs and Comments If you discover any problem due to the program however minor we would like to hear about it Please send e mail to mailto bernt guldbrandtsen agrsci dk Also if you succeed at compiling the program on platforms for which it is currently not available on the web page mentioned in section 5 w
10. pecified as 0000 for a diploid If one or both populations in a comparison have no data available at a locus a warning will be written If this is true for all loci for a comparison of two populations this will be indicated by that a string of stars appears in the output instead of a number 2 3 Polyploid Populations Polyploid populations are encoded exactly like diploid populations with the exception that the number of digits for each locus for each individual is changed from 4 to 2 times the ploidy level e g 6 digits for a triploid 8 digits for a tetraploid etc A simple triploid population might look like Pop Examplpop2 010101 010103 Examplpop2 010202 020203 Examplpop2 010101 020203 Since in general the number of copies of each allele in a polyploid cannot be observed directly genotypes must be padded with extra copies of alleles present in the genotype or with zeroes Le the following all for individuals genotypes each represent the same genotype Pop Examplpop2 010102 Examplpop2 010202 Examplpop2 010002 Examplpop2 020001 Likewise the followin all represent the same genotype Pop Examplpop2 010000 Examplpop2 000001 Examplpop2 010101 Examplpop2 010001 Calculating measures currently only works for the polyploid version of the Tomiuk amp Loeschcke measure and the Band Sharing Measure Hedrick s mea sure can also be used for comparing polyploid populations of the same level of ploidy Ho
11. se the r com mand You will be prompted for the number of the file to remove The numbers of the files currently selected are shown in the list of input files entered up to now The f command To make life easier if you want to calculate several measures for the same set of data files put the names of the data files into a file one name per line If you then use the command you will be prompted for the name of such a file with data files The p command If you just want to use the same data files as in the previous run use the p command It will cause POPDIST to read the file oldfiles tlh in the current directory This file was written at the end of the last run in this directory If the program hasn t been run in this directory before i e the file oldfiles t1h does not exist the command does nothing The o command Giving the o command will make the program prompt you for the name of a file where the genetics distance or similarity measures are to be written The q command Using this command causes the program to exit immedi ately The command This will show a brief summary of the commands The c command When you are done with selecting data files and optionally an output file use the c command to continue to the next screen 3 3 2 The Measure Selection Screen The Measure Selection screen consists of two parts e First the current choices are shown The choices consist of three things First the measure current
12. t be consistent across input files if several input files are to be used in the same run Genetic data are entered population by population Genetic data for one or more populations are given in one file but data for one population cannot be contained in more than one file 2 2 Data For One Population Data for one population are presented by one line containing the keyword pop at the beginning of a line After that follow lines containing data for one individual each Each individual line begins with a designation identifying the population that this individual belongs to This designation for the first individual is used by the program as the label for this population Designations for subsequent individuals are ignored The designation field is separated from the genotypes by a comma To the right of the comma are a number of fields equal to the number of loci The fields are separated by spaces or tab characters Each field consists of an even number of digits The number of digits is two times the ploidy level in the population i e in a diploid population there will be 4 digits for each locus in a triploid 6 digits and so forth Each pair of digits shows what allele a particular gene belongs to An example of the data for a tiny population of diploids that has been typed for two loci with three alleles in each population would be Pop Examplpop1 0102 0103 Examplpop1 0101 0203 2 2 1 Missing Values Missing values are generally s
13. t to screenwidth characters for output Use the measure of Tomiuk amp Loeschcke 1991 1995 1983 Use the unweighted measure o 13 References CAVALLI SFORZA L L amp EDWARDS A W F 1967 Phylogenetic Analysis Models and Estimation Procedures Evolution 21 September 550 570 GOLDSTEIN D B RUIS LINARES A CAVALLI SFORZA L L amp FELDMAN M W 1995 An evaluation of genetic distances for use with microsatellite loci Genetics 139 463 471 HEDRICK P W 1971 A new approach to measuring genetic similarity Evolu tion 25 276 280 H rs D M 1984 Misuse and modification of Nei s genetic distance Syst Zool 33 238 240 Nel M 1972 Genetic distance between populations Amer Natur 106 283 292 NEI M 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals Genetics 89 583 590 NEI M TAJMa F amp TATENO Y 1983 Accuracy of estimated phylogenetic trees from molecular data II Gene frequency data J Mol Evol 91 153 170 RAYMOND M amp Rousset F 1995 GENEPOP version 1 2 a population genetics software for exact tests and ecumenicism J Heredity 86 248 249 REYNOLDS J WEIR B S amp COCKERHAM C C 1983 Estimation of the coancestry coefficient Basis for a short term genetic distance Genetics 105 767 779 ROGERS J S 1972 Measures of genetic similarity and genetic distance Pages 145 158 of Studies in Gene
14. their respective standard way If on the other hand the j option is use then the uncorrected mean of the individual jackknife estimates are given in each case this number is then followed by the jackknife standard error of the mean In some cases some comparisons may have no data In these cases the output values are replaced by Also comparisons may result in impossible values e g log 0 These are also represented by 4 An Example One data file called exmp11 dat will be used It contains the data shown below This is example 1 Enzymel Enzyme2 Pop Examplpop1 0102 0103 Examplpop1 0101 0204 Pop Examplpop2 0101 0103 Examplpop2 0102 0203 Examplpop2 0104 0203 To calculate the Tomiuk amp Loeschcke genetic distance use the command popdist exmpl1 dat The output should then be popdist version 1 0 built Fri Apr 17 11 04 53 NFT 1998 Tomiuk Loeschcke s Identity estimating measure Population Examplpop1 Examplpop2 Examplpop1 1 000 0 896 Examplpop2 0 896 1 000 apart from the version information and the date To use instead the distance reconstructing measure of 1972 including calculation of the jackknife of standard errors use the command popdist n d j exmpl1 dat to obtain Nei 72 s distance reconstructing measure Population Examplpop1 Examplpop2 Examplpopi 0 000 0 000 0 126 0 067 Examplpop2 0 126 0 067 0 000 0 000 Next an example involving one diploid populati
15. tics VII Univ Texas Publ 7213 TAKEZAKI N amp NEI M 1996 Genetic distances and reconstruction of phy logenetic trees from microsatellite DNA Genetics 144 389 399 Tomiuk J amp LOESCHCKE V 1991 A new measure of genetic identity between populations of sexual and asexual species Evolution 45 1685 1694 TOMIUK J amp LOESCHCKE V 1995 Genetic identity combining mutation and drift J Heredity 74 607 615 Tomiuk J amp LOESCHCKE V 1996 A maximum likelihood estimator of the genetic identity between polyploid species J Theor Biol 179 51 54 TOMIUK J GULDBRANDTSEN B amp LOESCHCKE V 1998 Population dif ferentiation through mutation and drift A comparison of genetic identity measures Genetica 102 103 545 558 14
16. wever this measure is currently not supported directly by the pro gram It can be calculated assigning each genotype a 4 digit code unique within each locus and then running the program choosing Hedrick s measure as though the population were diploid In this format the triploid population shown above might be coded as Pop Examplpop3 0101 0101 Examplpop3 0102 0102 Examplpop3 0101 0102 3 Running the Program The program can be launched from a command line under MS DOS or UNIX On the Macintosh it is launched by double clicking the program icon If you are using a Macintosh skip forward to section 3 3 for a description of the menus 3 1 Specifying Input Files Files containing the data for the populations to be examined can be specified on the command line just by specifying their names Alternatively they can be specified in a file one name of an input file on each line POPDIST is then launched with the f option followed by the name of the file containing the filenames A third possibility is to use the same set of input files as was used with the last run of POPDIST in the current directory This is done by specifying the 0 option These three possibilities can be combined Any duplicates will automatically be ignored When POPDIST terminates it writes the names of the files used to the file oldfiles t1h in the current directory It is the content of this file that is read when using the 0 option is used in a lat
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