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Genomic Basis and Tradeoffs of Gigantism in the Capybara

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Genomic Basis and Tradeoffs of Gigantism in the Capybara bioRxiv preprint doi: https://doi.org/10.1101/424606; this version posted September 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 How to make a rodent giant: Genomic basis and tradeoffs of 2 gigantism in the capybara, the world’s largest rodent 3 4 Authors: 5 Santiago Herrera-Álvarez*1, Elinor Karlsson2, Oliver A. Ryder3, Kerstin Lindblad-Toh2,4, & 6 Andrew J. Crawford1 7 8 Affiliations: 9 1 Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia 10 2 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA 11 3 San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, 92027, USA 12 4 Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 13 752 36 Uppsala, Sweden. 14 15 *Corresponding author: 16 Address: Universidad de los Andes 17 Calle 19 No. 1-60, Bogotá, código postal 111711, Colombia, South America. 18 Email: [email protected] 19 Phone: +1(312) 536-1206 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/424606; this version posted September 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 22 Abstract 23 Gigantism is the result of one lineage within a clade evolving extremely large body size 24 relative to its small-bodied ancestors, a phenomenon observed numerous times in 25 animals. Theory predicts that the evolution of giants should be constrained by two 26 tradeoffs. First, because body size is negatively correlated with population size, purifying 27 selection is expected to be less efficient in species of large body size, leading to a 28 genome-wide elevation of the ratio of non-synonymous to synonymous substitution rates 29 (dN/dS) or mutation load. Second, gigantism is achieved through higher number of cells 30 and higher rates of cell proliferation, thus increasing the likelihood of cancer. However, 31 the incidence of cancer in gigantic animals is lower than the theoretical expectation, a 32 phenomenon referred to as Peto’s Paradox. To explore the genetic basis of gigantism in 33 rodents and uncover genomic signatures of gigantism-related tradeoffs, we sequenced the 34 genome of the capybara, the world’s largest living rodent. We found that dN/dS is 35 elevated genome wide in the capybara, relative to other rodents, implying a higher 36 mutation load. Conversely, a genome-wide scan for adaptive protein evolution in the 37 capybara highlighted several genes involved in growth regulation by the insulin/insulin- 38 like growth factor signaling (IIS) pathway. Capybara-specific gene-family expansions 39 included a putative novel anticancer adaptation that involves T cell-mediated tumor 40 suppression, offering a potential resolution to Peto’s Paradox in this lineage. Gene 41 interaction network analyses also revealed that size regulators function simultaneously as 42 growth factors and oncogenes, creating an evolutionary conflict. Based on our findings, 43 we hypothesize that gigantism in the capybara likely involved three evolutionary steps: 1) 44 Increase in body size by cell proliferation through the ISS pathway, 2) coupled evolution 45 of growth-regulatory and cancer-suppression mechanisms, possibly driven by 46 intragenomic conflict, and 3) establishment of the T cell-mediated tumor suppression 47 pathway as an anticancer adaptation. Interestingly, increased mutation load appears to be 48 an inevitable outcome of an increase in body size. 49 2 bioRxiv preprint doi: https://doi.org/10.1101/424606; this version posted September 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 50 Author Summary 51 The existence of gigantic animals presents an evolutionary puzzle. Larger animals have 52 more cells and undergo exponentially more cell divisions, thus, they should have 53 enormous rates of cancer. Moreover, large animals also have smaller populations making 54 them vulnerable to extinction. So, how do gigantic animals such as elephants and blue 55 whales protect themselves from cancer, and what are the consequences of evolving a 56 large size on the ‘genetic health’ of a species? To address these questions we sequenced 57 the genome of the capybara, the world’s largest rodent, and performed comparative 58 genomic analyses to identify the genes and pathways involved in growth regulation and 59 cancer suppression. We found that the insulin-signaling pathway was involved in the 60 evolution of gigantism in the capybara. We also found a putative novel anticancer 61 mechanism mediated by the detection of tumors by T-cells, offering a potential solution 62 to how capybaras mitigated the tradeoff imposed by cancer. Furthermore, we show that 63 capybara genome harbors a higher proportion of slightly deleterious mutations relative to 64 all other rodent genomes. Overall, this study provides insights at the genomic level into 65 the evolution of a complex and extreme phenotype, and offers a detailed picture of how 66 the evolution of a giant body size in the capybara has shaped its genome. 3 bioRxiv preprint doi: https://doi.org/10.1101/424606; this version posted September 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 67 Introduction 68 Body size is arguably the most apparent characteristic when studying multicellular life, 69 and understanding how and why body size evolves has been a major question in biology 70 [1]. Body size is a canonical complex trait, and, consequently, ontogenetic changes 71 underlying body size evolution affect other life-history traits, such as fecundity and 72 longevity [2,3]. Yet, how size is developmentally controlled to generate species-specific 73 differences remains elusive. Although increase in body size has several selective 74 advantages [4], maximum body size in tetrapods appears to be determined mostly by 75 intrinsic biological constraints [5–7]. Two major tradeoffs in the evolution of large bodies 76 are the reduction in population size and the increased risk of developing growth- 77 associated diseases, such as cancer [8,9]. 78 79 Larger species have lower population densities [8], slower metabolic rates, longer 80 generation times, and a lower reproductive output [3]. Together these traits lead to an 81 overall reduction in the genetic effective population size (Ne) relative to small-bodied 82 species [10]. In a finite population, the interplay between selection and genetic drift 83 determines the fate of newly arisen mutations, and the strength of drift relative to 84 selection will largely depend on Ne [11]. In smaller populations, slightly deleterious 85 mutations are expected to accumulate at a higher rate than in larger populations, due to 86 stronger genetic drift relative to purifying selection, thus increasing the mutation load in 87 the population, which may increase the risk of extinction [12]. Furthermore, animals have 88 positive allometric scaling of number of cells in the body with overall body size [13]. 89 Thus, if every cell has an equal probability, however low, of becoming cancerous and 90 related species have equivalent cancer suppression mechanisms, the risk of developing 91 cancer should increase as a function of number of cells. Therefore, large species should 92 face a higher lifetime risk of cancer simply because large bodies contain more cells 93 [9,14]. Moreover, giant body sizes are achieved mainly by an accelerated post-natal 94 growth rate [15], which represents an increment in the rate of cell proliferation [16]. For a 95 given mutation rate, an elevated rate of cell proliferation accelerates the rate of 96 accumulation of mutations and, thus, increases the chances for a cell population of 97 becoming cancerous [17]. 98 4 bioRxiv preprint doi: https://doi.org/10.1101/424606; this version posted September 23, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 99 The continued existence of enormous animals, such as whales and elephants, implies, 100 however, that the evolution of gigantism must be coupled with the evolution of cancer 101 suppression mechanisms. In fact, the lack of correlation between size and cancer 102 incidence, known as Peto’s Paradox, suggests that large-sized species have mitigated the 103 inherent increase in cancer risk associated with the evolution of large bodies [9,14]. For 104 instance, genomes of the Asian and African elephants (Elephas maximus; Loxodonta 105 africana) and the bowhead whale (Balaena mysticetus), three of the largest living 106 mammals, revealed lineage-specific expansion of genes associated with tumor 107 suppression via enhanced DNA-damage response [18,19] and cell cycle control [20], 108 respectively. Thus, cancer selection, i.e., selection to prevent or postpone deaths due to 109 cancer at least until after attainment of reproductive maturity, is especially important as 110 animals evolve larger bodies and might account for the relative lower incidence of cancer 111 in large animals and the evolution of anticancer mechanisms [21].
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