Positive Selection and Enhancer Evolution Shaped Lifespan and Body Mass in Great Apes

Abstract

Within primates, the great apes are outliers both in terms of body size and lifespan, since they include the largest and longest-lived species in the order. Yet, the molecular bases underlying such features are poorly understood. Here, we leveraged an integrated approach to investigate multiple sources of molecular variation across primates, focusing on over 10,000 genes, including approximately 1,500 previously associated with lifespan, and additional approximately 9,000 for which an association with longevity has never been suggested. We analyzed dN/dS rates, positive selection, gene expression (RNA-seq), and gene regulation (ChIP-seq). By analyzing the correlation between dN/dS, maximum lifespan, and body mass, we identified 276 genes whose rate of evolution positively correlates with maximum lifespan in primates. Further, we identified five genes, important for tumor suppression, adaptive immunity, metastasis, and inflammation, under positive selection exclusively in the great ape lineage. RNA-seq data, generated from the liver of six species representing all the primate lineages, revealed that 8% of approximately 1,500 genes previously associated with longevity are differentially expressed in apes relative to other primates. Importantly, by integrating RNA-seq with ChIP-seq for H3K27ac (which marks active enhancers), we show that the differentially expressed longevity genes are significantly more likely than expected to be located near a novel "ape-specific" enhancer. Moreover, these particular ape-specific enhancers are enriched for young transposable elements, and specifically SINE-Vntr-Alus. In summary, we demonstrate that multiple evolutionary forces have contributed to the evolution of lifespan and body size in primates.

Keywords: ageing; apes; cancer; cell senescence; cis-regulatory evolution; evolutionary genomics; natural selections; transposable elements.

Fig. 1.

The evolution of BM and MLS across primates. (a) PGLS models correlating MLS ∼ BM across mammals. The highlighted species are from the primate order (orange) and other lineages that have been previously associated with cancer resistance and extreme longevity: bats (green), naked mole rat (NMR, red), cetaceans (dark gray). (b) PGLS correlating MLS ∼ BM across primates. The dashed lines represent a positive correlation between log10-transformed BM and MLS. The continuous line displays the correlation between great apes and other primates. (c) Phylogenomic design. The molecular evolution analysis included 19 mammalian species. The six species highlighted are representatives from the main primate lineages (Catarrhini, Platyrrhini, and Strepsirrhini). For these six species, RNA-seq and ChIP-seq data were publicly available (Trizzino et al. 2017). The colors in the phylogenetic tree reflect the values of MLS and BM in each primate branch respectively, from lowest (red) to highest (blue).

Fig. 2.

Examples of genes whose evolution correlated with the evolution of MLS. (a, b) Ingenuity Pathway Analysis for 276 genes whose rates of evolution are positively correlated with the MLS. Panels (a) and (b), respectively, show enriched categories for cancer and developmental pathways. (c) Independent PGLS models were performed in order to evaluate the independent contribution of each gene in the evolution of MLS across primates (PGLS dN/dS ∼ MLS). The dN/dS values were obtained from the branch model in PAML. The genes with a FDR <0.1 were considered statistically significant.

Fig. 3.

Genes under positive selection exclusively in the great ape ancestor (a–g): IRF3-CL, SCRN3, GASK1B, DIAPH2, and SELENOS. The color gradients are used to display the degree and typology of amino acid change. The bars indicate the positive sites under the Bayes Empirical Bayes (BEB) analysis with a foreground lineages Prob(ω > 1): *** (red), ** (orange), and * (gray).

Fig. 4.

Evolution of longevity GE in the primate liver. (a) Venn diagram representing the total number of orthologous longevity genes (1,539) shared by at least one species in each of main primate lineages, broken down based on the different categories (tumor suppressors, oncogenes, CS and ageing genes). The genes were divided into categories: ageing, senescence-related genes, tumor suppressor genes (TSGs), and oncogenes. (b) Expression levels for the 1,539 genes in the liver were comparable across primates. (c) Expression levels for ageing-related genes and senescence genes. (d) Expression levels for ageing-related genes, tumor suppressors, and oncogenes. In both groups (c, d), humans display higher expression compared with other primates (Wilcoxon’s rank-sum test). (e) The expression of the 1,539 longevity genes in the liver is positively correlated between humans and chimpanzee (Spearman’s correlation coefficient, R = 0.53, P < 0.001). (f) Oncogenes are significantly more expressed in great apes compared with other primates. Senescence genes are significantly less expressed in great apes relative to the other primates (Wilcoxon’s rank-sum test, P < 0.05).

Fig. 5.

Ape-specific enhancers are enriched near differentially expressed longevity genes. (a) 27/122 differentially expressed (DE) longevity genes (22.1%) are located within 50 kb of an ape-specific enhancer (a total of 38 ape-specific enhancers for 27 DE genes). In comparison, only 4/122 (3.3%) randomly selected genes (1,000 permutations) are located within 50 kb of an ape-specific enhancer (permutation test P < 2.2×10⁻¹⁶). (b) 20/38 ape-specific enhancers (52%) located within 50 kb of the DE longevity genes overlap annotated TEs. (c) Of the DE longevity genes found near TE-derived ape-specific enhancers, 65% were identified as upregulated, 35% as downregulated (Fisher’s exact test P = 0.0425). (e) LTR and SVA transposons are overrepresented in the sequence of the ape-specific enhancers located within 50 kb of a DE longevity gene (Fisher’s exact test P < 2.2×10⁻¹⁶ for SVAs; P < 0.0001 for LTRs).