Appendix III.

Gene flow-related software

Prepared by Rodney Dyer, Juan Fernandez, and Victoria Sork
Below is a set of gene flow-related software programs collected by Rodney Dyer, Juan Fernandez, and Victoria Sork (in that order) with technical help from Deby DeWeese and Bruce Satow at NCEAS.  These software were collected as part of the Gene flow workshop held at NCEAS on January 5-9, 1998.  Most of these software can be obtained directly or indirectly through the web page for the gene flow workshop proceedings available through the NCEAS webpage ( http: www.NCEAS.ucsb.edu).  While we have reviewed many programs additional to those below, we included only the ones that seem to be relevant and of acceptable quality.  New programs may be available that are of equal quality and updates of these programs may emerge after the preparation of this collection.  For that information, you must search the web directly.     (V. Sork, 1 May 1998).
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1)  Migrate, v.0.3 documentation or Migrate, v.0.3 download  (Connects to website)
Platform:  Assorted, includingWindows 95, Macintosh, Sun, Linux, and source code.
by Peter Beerli, University of Washington, Dept. of Genetics

    Migrate estimates population parameters (effective population size and migration rates) using genetic data (electrophoretic markers, microsatellite markers, sequence data). Migrate is a subset of LAMARC. The current version of Migrate uses a simple two population model with four parameters.
 
 
2)  PollenGF.    (Downloads files)
Platform:  Macintosh
by John Nason, University of Iowa.

      PollenGF uses paternity exclusion techniques to estimate apparent gene flow using progeny arrays from maternal plants.  Gene flow can be calculated for individual mothers or local population.  Sample data and output are included.
 

3)  FijAnal version 2.1  (Downloads files)
Platform:  Macintosh
by John Nason, University of Iowa.

    FijAnal is a program to conduct spatial analysis of kinship or coancestry.  " In order to obtain a more powerful test for fine-scale, spatial genetic structure, genetic correlations between individuals can be summarized over a range of distance intervals in terms of a multilocus estimate of kinship (Barbujani 1987) or coancestry (Cockerham 1969). In contrast to Moran's I, genetic structure statistics, such as the kinship coefficient, have a well developed foundation in population genetics theory and provide a natural means of combining data over alleles at a locus and over loci (Heywood 1991). Further, a spatial autocorelation approach permits the investigation of genetic structure at much finer distance intervals than estimators of genetic differentiation, such as Wright's Fst that quantify gene frequency variation among quadrats rather than individuals."
 

4) BS_fij version 2.1   (Downloads files)
Platform:  Macintosh
by John Nason, University of Iowa.

    "In the program BS_fij, tests of significance are performed by using randomization procedures to generate populations under the null hypothesis of no spatial genetic structure, Ho: fij=0 (see Slatkin and Arter [1991] for a general discussion of this approach). In this procedure, map locations occupied by the individuals in the population, or the subset of the population under examination, are randomly assigned intact multilocus genotypes drawn at random with replacement from the sample population. "  This program must be run with analyses from FijAnal.
 

5)  Rst Calc  (Downloads files)
Platform:  PC
by Simon Goodman, University of Edinburgh

Goodman SJ (1997), RST CALC: A collection of computer programs for  calculating unbiased estimates of genetic differentiation  and determining their significance for microsatellite data.  (Molecular Ecology 6:881-885).

      This collection of programs carry out the following functions:
i) Calculates Rho, an unbiased estimator of Slatkin's (1995; Genetics 139: 457-462) Rst. Estimates are provided for both individual loci and over all loci, calculated across total populations and for all pairwise population comparisons.
ii) Determines if overall Rho values across loci are significantly different from zero by permutation tests and uses bootstrapping to provide 95% confidence intervals, mean bootstrap Rho, plus the variance and SE of the bootstrap mean Rho.
iii) Calculates Goldstein et als (delta-mu)^2 genetic distance measure for  microsatellites.
 
 
 6)  Patsim  1.2 . Paternity Analysis Simulation program  (Downloads files)
Platform:  PC Windows
by (C) 1996 Tristan Marshall, University of Edinburgh

A description of the program and its uses can be found in:  Marshall, T.C., Slate, J., Kruuk, L. and Pemberton, J.M. (in prep). Statistical confidence for likelihood-based paternity inference in natural populations.
 
 
7)   GENFLOW.  A computer program for estimating levels of pollen contamination in clonal seed orchards.  (Downloads files)
Platform:  PC
by W. T. Adams and J. Burczyk
Department of Forest Science, Oregon State University
Department of Genetics, Institute of Dendrology, Polish Academy of Sciences

    "GENFLOW was developed to estimate pollen contamination levels in seed orchards of conifers using electrophoretic data. The multilocus estimation procedure is described in detail in Smith and Adams (1983), Adams and Birkes (1991), and Adams et al. (1992)." The set of programs includes a manual under the name GENFLOW.WP.
 

8)  NEIGHBOR. A computer program for estimating mating patterns in conifer populations from genetic marker data. (Downloads files)
Release 1. 1993. Oregon State University, Oregon, USA
Platform:  PC
by J. Burczyk1, W.T. Adams2, and D.S. Birkes3

1 Department of Biology and Environment Protection, Pedagogical University, Chodkiewicza
   51, 85-064 Bydgoszcz, Poland, e-mail: burczyk@mail.atr.bydgoszcz.pl , Fax : (52) 41-34-64
2 Department of Forest Science, Oregon State University, Corvallis, Oregon 97331, USA
3 Department of Statistics, Oregon State University, Corvallis, Oregon 97331, USA

     "The computer program, NEIGHBOR, was written so that mating system parameters in the neighborhood model (Adams and Birkes, 1991) can be estimated for conifer populations. Application of the model requires observations on multi-locus genetic markers in the haploid pollen gametes of offspring from individual mother trees of known genotype. The model assumes that pollen successful in fertilizing viable offspring is derived from three sources: self-fertilization, cross-fertilization with nearby males in an arbitrary defined neighborhood, and cross-fertilization with males from outside the neighborhood (gene flow). Besides accounting for levels of self-fertilization and background pollination (mating with distant males), the model is useful for investigating relationships between mating success of males within neighborhoods and factors expected to influence male-mating success; including distance to mother trees, relative fecundity of males, flowering phenology synchronization (see below), and interaction between these factors."   The set of programs includes a manual with complete description.
 
 
9)  Gilpin PopGen Java Applets (link to web page: http://insci14.ucsd.edu/~bi178s/genetics)
Platform:  Java
by Michael Gilpin, University of California-San Diego
 

  • These simple, fast applets illustrate graphically a number of the dynamical processes of population genetics.  They are useful for teaching and demonstration purposes.  Rather than link them individually, the link is set up to Gilpin's web page where you can get them.
  •  
     

      THE THREE PROGRAMS BELOW WERE OBTAINED THROUGH THE
    HOME PAGE OF MONTY SLATKIN

    10)  immance.c.   (Downloads files from NCEAS website)
    Platform:  PC
    by Bruce Rannala and Joanna Mountain.
     
     "immanc.c is a program designed to test whether or not an individual is an immigrant or is of recent immigrant ancestry.  This test is described in detail in the following article: Rannala, B and Mountain, J.L. (1997) Detecting immigration by using multilocus genotypes. Proc. Natl Acad Sci, USA 94:9197-9201.  In order to apply the test, one must have genotype data for multiple loci for multiple individuals of two or more populations (see section on input file below).  Ideally, but not necessarily, all individuals have been tested for all polymorphisms.  The method is appropriate for use with allozyme, microsatellite, or restriction fragment length data."
     

    11)  Slatkin's Isolation by Distance Program(Downloads files from NCEAS)
    Platforms:  PC, Unix
    by M. Slatkin.

    This program will  estimate pairwise levels of gene flow  and regress the estimated level of gene flow, M^, on geographic distance.  The following is excerpted from Slatkin's documentation:

    "What follows this text is a program I have written to estimate levels of gene flow between pairs of sampling locations.  There is also a sample input and two sample output files that I will describe later.  This is based on the program.  I used to produce the figures in my paper "Isolation by distance in equilibrium and non-equilibrium populations" which appeared in Evolution (47(1): 264-279; 1993). "
     

    12)  PMLE12.  Pseudo Maximum Likelihood Estimator of Gene Flow
    (Downloads folder from NCEAS or download individual files for Mac or Windows 3.1 below)
    Platforms:  Mac PowerPC, Windows
    by Bruce Rannala and Hartigan

    Excerpted from documentation for program PMLE12, version 1.2, April 3, 1996:

    "This program estimates the gene flow parameter theta for a collection of two or more semi-isolated populations by (pseudo) maximum likelihood using either allozyme or mtDNA RFLP data. The method is described in a paper by Rannala and Hartigan, Genetical Research 67: 147-158 (1996).
     


    13) Arlequin. (URL: http://anthropologie.unige.ch/text/arlequin/) A software for population genetic data analysis. Platforms: Windows 95 or Windows NT

    Citations:

    1. Excoffier, L, Smouse, PE, and Quattro, JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131:479-491.

    2. Schneider, S, Roessli, D, and Excoffier, L. 1999. Arlequin ver 2.0: A software for population genetic data analysis., . Univ of Geneva Genet. Biometr. Lab: Geneva, Switzerland.

    Excepts from web site.

    "Arlequin is an exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). A variety of population genetics methods have been implemented either at the intra-population or at the inter-population level, and they can be conveniently selected and parameterized through a graphical interface. Arlequin has no equivalent in his field and will be extremely useful to analyzed the large data sets which are now available by the use of the latest molecular engineering techniques."

    "Arlequin's WWW site was officially opened on June 15th, 1996. It is hosted by the Department of

    Anthropology & Ecology of the University of Geneva. Arlequin's beta testing period ended on January 31st, 1997 at midnight - time at which version "1-point-oh-no" was released to the scientific community of planet earth!! December 17th, 1997, less than a year later, version 1.1, a significant update, was uploaded to to its web site. The same week, Arlequin's Official User Manual was released in Adobe Acrobat Format."

     


     
    14) Bottleneck version 1.1.03  (27.XI.97)

    Platforms: Code written with Delphi 2.0® for Windows95® by Sylvain Piry
     Conception : Jean-Marie Cornuet and Gordon Luikart.

    Bottleneck is a program for detecting recent effective population size reductions from allele
    data frequencies.

    "The program BOTTLENECK computes for each population sample and for each locus the distribution of the heterozygosity expected from the observed number of alleles (k), given the sample size (n) under the assumption of mutation-drift equilibrium. This distribution is obtained through simulating the coalescentprocess of n genes under two possible mutation models, the IAM and the SMM. This enables the computation of the average (Hexp) which is compared to the observed heterozygosity (Hobs, in the sense of Nei's gene diversity) to establish whether there is an heterozygosity excess or deficit at this locus. In addition, the standard deviation (SD) of the mutation-drift equilibrium distribution of the heterozygosity is used to compute the standardized difference for each locus ((Hobs-Hexp)/SD). The distribution obtained through simulation enables also the computation of a P-value for the observed heterozygosity."
     
     

    15)  GDA: Software for the Analysis of Discrete Genetic Data  (Connects to website at http://chee.unm.edu/gda/)

     Platforms: Windows95, Windows NT
     by Paul O. Leiws and Dmitri Zaykin

    GDA (Genetic Data Analysis) is a Microsoft Windows program for analyzing discrete genetic data. Both 16-bit versions (for Windows 3.1x) and 32-bit versions (for Windows 95 or Windows NT) are available. The NEXUS data file standard used by the phylogenetic analysis programs PAUP and MacClade has been extended (by the addition of the GDADATA block) to accommodate discrete genetic data. Data can be imported also in: a) BIOSYS format (types 1 or 2); b) Weir format, i.e., the format used used in the 1st edition of the book (see below); or c) GeneStrut format.

    DISCLAIMER: GDA is designed to accompany the second edition of Bruce Weir's book "Genetic Data Analysis" (1996. Sinauer Associates, Inc. Publishers, Sunderland, Massachusetts). The program was written independently of the book, and the authors of the computer program receive no royalties from sales of the book. The program GDA is thus offered simply as a service to the scientific community, and access to GDA is not included in the purchase price of the book "Genetic Data Analysis." Although the program GDA is, at present, being distributed freely, the authors reserve the right to seek compensation for future versions of the product. Note that the program is still in the development stage, meaning that new features are still being added and bugs are still being found on a regular basis.This product is offered on a use-at-your-own-risk basis: the authors assume no liability for loss or damage of any kind resulting from your use of this product.

     


     
      16) GENEPOP. Version 3.1d, March 1999.

    The software and documentation for this program can be downloaded from their website at ftp://ftp.cefe.cnrs-mop.fr/genepop/.

    GENEPOP is a software program than can provide a variety of population genetic analyses (see citations below). A description of the program is available in their documentation.

    Citations:

    Raymond, M. and F. Rousset. 1994. GenePop. ver 1.0. Institut. des Sciences de l'Evolution. Université de Montpellier, France.

    Raymond M. & Rousset F, 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249

    Goudet J, Raymond M, De Meeüs T and Rousset F, 1996. Testing differentiation in diploid populations. Genetics 144:1933-1940.

    Raymond M and Rousset F, 1995. An exact test for population differentiation. Evolution 49:1280-1283.

    Rousset F and Raymond M, 1995. Testing heterozygote excess and deficiency. Genetics 140:1413-1419.

    Rousset F, 1996. Equilibrium values of measure of population subdivision for stepwise mutation processes. Genetics 142 :1357-1362.

    Rousset F, 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145 : 1219-1228.


     
     
     
     
     
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