Single-cell sequencing data have revealed that cellular phenotypes, such as gene expression states, are often low-dimensional, suggesting that cellular variation may arise from combinations of a smaller set of gene expression programs. A genome therefore defines a repertoire of cellular phenotypes that can be configured through different combinations of programs. However, organisms vary in how much of this repertoire is exposed to selection. In unicellular organisms, different phenotypes are often expressed across environments or life-cycle stages, so selection in a given context acts primarily through the phenotype expressed there. In multicellular organisms, multiple phenotypes can coexist within an individual and contribute jointly to fitness. Here, we use a geometric model to ask how selection acting through cellular phenotypes separately or jointly constrains the ability of a shared genome to evolve and maintain differentiated phenotypes across multiple functional demands. We vary the number of functional demands and how many corresponding phenotypes contribute jointly to fitness. We find similar evolutionary outcomes when demands are weakly divergent. Under strongly divergent demands, however, selection on one phenotype at a time leads to reduced differentiation as demands accumulate, even when sufficient programs are available. As more phenotypes contribute jointly to fitness, differentiation and performance improve. When all phenotypes contribute jointly, differentiation is maintained until demands outnumber programs. Our results suggest that how cellular phenotypes are organized in time and space can impose distinct constraints on the evolution of differentiation from a shared genome.
Kim, M., Pennell, M.
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