Macroorganisms are colonized by microbial communities that exert important biological and
ecological functions, the composition of which is subject to host control and has therefore
been described as “an ecosystem on a leash”. However, domesticated organisms such as
crop plants are subject to both artificial selection and natural selection exerted by the agricultural ecosystem. Here, we propose a framework for understanding how host control of the
microbiota is influenced by domestication, in which a double leash acts from domesticator to
host and host to microbes. We discuss how this framework applies to a plant compartment
that has demonstrated remarkable phenotypic changes during domestication: the seed.
