Mendel's accountant: A biologically realistic forward-time population genetics program

Abstract

Mendel's Accountant (hereafter referred to as "Mendel") is a user-friendly biologically realistic simulation program for investigating the processes of mutation and selection in sexually reproducing diploid populations. Mendel represents an advance over previous forward-time programs in that it incorporates several new features that enhance biological realism including: (a) variable mutation effect and (b) environmental variance that affects phenotype. In Mendel, as in nature, mutations have a continuous range of effect from lethal to beneficial, and may vary in expression from fully dominant to fully recessive. Mendel allows mutational effects to be combined in either a multiplicative or additive manner to determine overall genotypic fitness and provides the option of either truncation or probability selection. Environmental variance is specified via a heritability parameter and a non-scaling noise standard deviation. Mendel is computationally efficient, so many problems of interest can be run on ordinary personal computers. Parallelized using MPI, Mendel readily handles large population size and population substructure on cluster computers. We report a series of validation experiments which show consistently that Mendel results conform to theoretical predictions. Its graphical user interface is designed to make problem specification intuitive and simple, and it provides a variety of visual representations in the program output. The program is a versatile research tool and is useful also as an interactive teaching resource.