Fig. 1

Schematic diagram of a disease transmission experiment. a The experiment consists of several contact groups in which some individuals are initially infected “seeders” and some are initially susceptible “contacts”. Each symbol represents an individual, and the annotations AA, AB and BB refer to the genotype of that individual at a given bi-allelic SNP under investigation. b As the experiment progresses some susceptible individuals become infected and some infected individuals recover. c If the experiment continues until the epidemics die out, only susceptible and recovered individuals are observed in the final state (for practical reasons, experiments are often terminated before this point). Note that the spatial separation of seeders (left) and contacts (right) in this diagram is for illustrative purposes only (random mixing between individuals is assumed)