Horizontal Gene Transfer Leads to Increased Task Acquisition and Genomic Modularity in Digital Organisms

Biological organisms exhibit a tremendous range of diversity across many different scales. At a genetic level, one of the starkest distinctions is between how genetic material is arranged in prokaryotes (such as bacteria) and eukaryotes (such as plants and animals). When a given biological process, such as enzymatic degradation of an energy source, requires several steps, it is common in eukaryotes for the genes encoding these steps to be widely dispersed through the organism’s genome, though perhaps not as widely as would be expected from a purely random distribution (Lee and Sonnhammer, 2003). In contrast, bacterial genomes are typically arranged in operons, where some or all of the components needed for a particular function are found together in one section of the genome (Land et al., 2015). What might account for this difference in genome organization? One intriguing possibility is that the greater extent of genome modularity in bacteria could be driven by horizontal gene transfer (HGT). HGT refers to a set of ways in which organisms can acquire genetic material from a source other than their direct parent(s), whether through ingesting nucleic acids as energy sources, accepting a plasmid from another cell, or even having nucleic acids injected by a virus (Soucy et al., 2015). HGT is generally seen as pervasive in bacteria, while considered less common in eukaryotes (Maddamsetti and Lenski, 2018; Koonin, 2016). Because HGT can insert genes into new host organisms, it provides a potential selective benefit toward genomic arrangements where the instructions needed for a particular function are arranged compactly. An organism with all of the information needed for a complete function is more likely to manage to spread this genetic material via HGT if that material is localized to one genomic segment, instead of being diffuse throughout the genome (Lawrence, 1999; Lawrence and Roth, 1996). This very spread of information via HGT could even act to make bacterial genomes more modular (Kreimer et al., 2008). These processes can reinforce each other – a more modular genome makes for more effective HGT, which then causes the resulting genomes to be even more modular. Testing the evolutionary impacts of either allowing or disallowing particular types of mutations is exceptionally difficult in physical organisms. Therefore, we chose to address these questions by harnessing the power of digital evolution.