How to Make a Rodent Giant: Genomic Basis and Tradeoffs of Gigantism in the Capybara, the World’s Largest Rodent

Gigantism is the result of one lineage within a clade evolving extremely large body size relative to its small-bodied ancestors, a phenomenon observed numerous times in animals. Theory predicts that the evolution of giants should be constrained by two tradeoffs. First, because body size is negatively correlated with population size, purifying selection is expected to be less efficient in species of large body size, leading to a genome-wide elevation of the ratio of non-synonymous to synonymous substitution rates (dN/dS) or mutation load. Second, gigantism is achieved through higher number of cells and higher rates of cell proliferation, thus increasing the likelihood of cancer. However, the incidence of cancer in gigantic animals is lower than the theoretical expectation, a phenomenon referred to as Peto’s Paradox. To explore the genetic basis of gigantism in rodents and uncover genomic signatures of gigantism-related tradeoffs, we sequenced the genome of the capybara, the world’s largest living rodent. We found that dN/dS is elevated genome wide in the capybara, relative to other rodents, implying a higher mutation load. Conversely, a genome-wide scan for adaptive protein evolution in the capybara highlighted several genes involved in growth regulation by the insulin/insulin-like growth factor signaling (IIS) pathway. Capybara-specific gene-family expansions included a putative novel anticancer adaptation that involves T cell-mediated tumor suppression, offering a potential resolution to Peto’s Paradox in this lineage. Gene interaction network analyses also revealed that size regulators function simultaneously as growth factors and oncogenes, creating an evolutionary conflict. Based on our findings, we hypothesize that gigantism in the capybara likely involved three evolutionary steps: 1) Increase in body size by cell proliferation through the ISS pathway, 2) coupled evolution of growth-regulatory and cancer-suppression mechanisms, possibly driven by intragenomic conflict, and 3) establishment of the T cell-mediated tumor suppression pathway as an anticancer adaptation. Interestingly, increased mutation load appears to be an inevitable outcome of an increase in body size. Author Summary The existence of gigantic animals presents an evolutionary puzzle. Larger animals have more cells and undergo exponentially more cell divisions, thus, they should have enormous rates of cancer. Moreover, large animals also have smaller populations making them vulnerable to extinction. So, how do gigantic animals such as elephants and blue whales protect themselves from cancer, and what are the consequences of evolving a large size on the ‘genetic health’ of a species? To address these questions we sequenced the genome of the capybara, the world’s largest rodent, and performed comparative genomic analyses to identify the genes and pathways involved in growth regulation and cancer suppression. We found that the insulin-signaling pathway was involved in the evolution of gigantism in the capybara. We also found a putative novel anticancer mechanism mediated by the detection of tumors by T-cells, offering a potential solution to how capybaras mitigated the tradeoff imposed by cancer. Furthermore, we show that capybara genome harbors a higher proportion of slightly deleterious mutations relative to all other rodent genomes. Overall, this study provides insights at the genomic level into the evolution of a complex and extreme phenotype, and offers a detailed picture of how the evolution of a giant body size in the capybara has shaped its genome.