Digital Organism Simulation Environment (DOSE): A Library for Ecologically-Based In Silico Experimental Evolution

Abstract

Testing evolutionary hypothesis in biological setting is expensive and time consuming. Computer simulations of organisms (digital organisms) are commonly used proxies to study evolutionary processes. A number of digital organism simulators have been developed but are deficient in biological and ecological parallels. In this study, we present DOSE (Digital Organism Simulation Environment), a digital organism simulator with biological and ecological parallels. DOSE consists of a biological hierarchy of genetic sequences, organism, population, and ecosystem. A 3-character instruction set that does not take any operand is used as genetic code for digital organism, which the 3-nucleotide codon structure in naturally occurring DNA. The evolutionary driver is simulated by a genetic algorithm. We demonstrate the utility in examining the effects of migration on heterozygosity, also known as local genetic distance