Modeling Population Genetics

Abstract

P opulation genetics relies heavily on mathematical modeling to make quantitative predictions about the behavior of genes in populations. These models are based on the principles of classic Mendelian gene inheritance; the Hardy-Weinberg equilibrium law, which predicts the gene frequency in a population; and Darwin's theory of natural selection. PopGene version 1 is a simulation program that explores the parameters that affect the behavior of alternative forms of a gene (alleles) in a population. The program window is composed of three smaller windows specifying the parameters used, the calculated allele frequencies through each generation, and the graphical output of the calculations. PopGene provides simulations for both basic and more advanced models in population genetics. The simplest model demonstrates the principles of the Hardy-Weinberg equilibrium law for the case of a single gene with two alleles. Increasingly complex examples based on the assumptions of the Hardy-Weinberg equilibrium law demonstrate the effect of multiple alleles of a gene and multiple gene loci on the genotype of all the individuals in a population. Default parameters for each model are built into the program, but users may also enter their own values. The simulation results, parameters, and graphs may be saved or printed. Up to 15 simulations may be run for a particular model with the results plotted on a single graph for easy comparison. Natural selection and inbreeding can be studied with the program. Natural selection of a gene with two alleles occurs when the fitness of each genotype is not equal. The program permits users to examine the outcomes of several scenarios—selection of an allele that exhibits dominance over another, alleles that combine to produce an intermediate (semidominant) phenotype, an allele that is recessive to another, or selection against a recessive allele because of its lethality. The model for inbreeding explores the consequence of nonrandom mating between individuals on the genotype frequencies of that population. Mating pairings are included to demonstrate self-fertilization (the most extreme form of nonrandom mating), as well as matings between parent and offspring; matings between siblings, first cousins, and second cousins; and random mating. PopGene also provides simulations for genetic drift, mutation, and migration—factors that contribute to evolutionary changes in a population that have long-term effects and are more difficult to study. In summary, PopGene is a valuable tool to use in conjunction with traditional textbook-based teaching of an introductory population genetics course. It provides students with illustrations of the principles they have learned. The program is straightforward, easy to use, and is available for Macintosh and Windows platforms. No preprinted manual is available for PopGene; however, a concise and well-written one is supplied as a PDF file that is readable with Adobe Acrobat. It covers the specifics of using the program and provides a step-by-step tutorial. A brief summary of population genetics, mathematical modeling, and the value and limitations of computer simulations is also discussed. The system requires a PC with a 486 or Pentium processor that uses Windows 3.1, 95, 98, or NT with 8 MB RAM or any Macintosh with 4 MB RAM, a 1.4-MB disk drive, and a hard drive. PopGene Trinity Software, Inc. Plymouth, NH. $95.00; $39.95, college students. 800-352-1282