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

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.