Genetics is traditionally understood as the study of how an individual's phenotype is affected by its own genotype. However, in recent years it has become clear that the genotypes of the individual's social partners (relatives and peers) and the genetic makeup of the individual's microbiota are also important. Furthermore, commensal microbes can be exchanged between socially interacting conspecifics. Therefore, we believe the individual should be studied not in isolation but, instead, together with its social partners and microbiota, which we refer to as the "Hologenome 2.0".
I will discuss the expected evolutionary consequences of the Hologenome 2.0 and present the empirical strategies we are developing to study it, using genetically diverse (outbred) and deeply phenotyped laboratory rodents as study system. We have already uncovered widespread and, in some cases, strong genetic effects arising from social partners (cage mates), and pinpointed specific genes involved. We are now developing an approach to gain insights into the traits of conspecifics that are most influential, leveraging the phenome-wide data available in our rodent cohorts to do so. We have also studied host/microbiome interactions in thousands of outbred rats, and have started developing methods to quantify and characterise microbial transmission between cage mates.