Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system

Abstract

T cells are a type of white blood cell that play a critical role in the immune response against foreign pathogens through a process called T Cell Adaptive Immunity (TCAI). However, the evolution of the genes and nucleotide sequences involved in TCAI is not well understood. To investigate this, we performed comparative studies of gene annotations and genome assemblies of 28 vertebrate species and identified sets of human genes that are involved in TCAI, carcinogenesis, and ageing. We found that these gene sets share interaction pathways which may have contributed to the evolution of longevity in the vertebrate lineage leading to humans. Our human gene age dating analyses revealed that there was rapid origination of genes with TCAI-related functions prior to the Cretaceous eutherian radiation and these new genes mainly encode negative regulators. We identified no new TCAI-related genes after the divergence of placental mammals, but we did detect an extensive number of amino acid substitutions under strong positive selection in recently evolved human immunity genes suggesting they are co-evolving with adaptive immunity. More specifically, we observed that antigen processing and presentation and checkpoint genes are significantly enriched among new genes evolving under positive selection. These observations reveal an evolutionary process of T Cell Adaptive Immunity that were associated with rapid gene duplication in the early stages of vertebrates and subsequent sequence changes in TCAI-related genes. These processes together suggest an early genetic construction of the vertebrate immune system and subsequent molecular adaptation to diverse antigens.

Keywords: T Cell Adaptive Immunity; ageing; new gene evolution; sequence substitution; vertebrate genomes.

Fig. 1.

The longevity, age of maturation, and adult weight of animal species. The log value of longevity (years), female maturation age (days), male maturation age (days), and adult weight (grams) are plotted against the divergence of the corresponding species to human in (A). Otherwise, animal species are clustered in different orders and plotted (B).

Fig. 2.

The collection of TCAI, TS, OG, and aging genes. There was little categorical overlap of TCAI, TS, OG, and aging genes (A). Reactome pathway overlap of TCAI, TS, OG, and aging genes (B). NHGRI GWAS catalog overlap (C). For details on the Reactome and NHGRI GWAS overlap, see supplementary table S10, Supplementary Material online. (D) Enrichment results for Reactome pathway and NHGRI GWAS Catalog.

Fig. 3.

The age dating of human genes. Human genes are grouped into different categories including total, TCAI, TS, OG, and aging genes and assigned to different branch groups based on divergence time. Compared with total genes, significantly less or equal amount of TCAI, TS, OG, and aging genes emerged in each branch. ***Gene numbers are slightly different from synteny-based gene age assignment.