Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses

Abstract

Disease susceptibility and resistance are important factors for the conservation of endangered species, including elephants. We analyzed pathology data from 26 zoos and report that Asian elephants have increased neoplasia and malignancy prevalence compared with African bush elephants. This is consistent with observed higher susceptibility to tuberculosis and elephant endotheliotropic herpesvirus (EEHV) in Asian elephants. To investigate genetic mechanisms underlying disease resistance, including differential responses between species, among other elephant traits, we sequenced multiple elephant genomes. We report a draft assembly for an Asian elephant, and defined 862 and 1,017 conserved potential regulatory elements in Asian and African bush elephants, respectively. In the genomes of both elephant species, conserved elements were significantly enriched with genes differentially expressed between the species. In Asian elephants, these putative regulatory regions were involved in immunity pathways including tumor-necrosis factor, which plays an important role in EEHV response. Genomic sequences of African bush, forest, and Asian elephant genomes revealed extensive sequence conservation at TP53 retrogene loci across three species, which may be related to TP53 functionality in elephant cancer resistance. Positive selection scans revealed outlier genes related to additional elephant traits. Our study suggests that gene regulation plays an important role in the differential inflammatory response of Asian and African elephants, leading to increased infectious disease and cancer susceptibility in Asian elephants. These genomic discoveries can inform future functional and translational studies aimed at identifying effective treatment approaches for ill elephants, which may improve conservation.

Keywords: EEHV, tuberculosis, genomes; cancer; conservation; disease; elephants.

Fig. 1.

Accelerated regions in elephant genomes. (a) Using a whole genome alignment of 12 mammals we defined genomic regions that were accelerated (ARs) in two elephant species (red), yet conserved in the set of background species (blue). Branch lengths are given in terms of mean substitutions per site at 4-fold degenerate sites (neutral model). (b) Among the ARs detected in elephants, we found ARs common to both elephant species as well as ARs specific to either Asian or African bush elephants. (c) Differentially expressed (DE) genes were much more likely to be found in Asian elephant-specific (Fisher’s Exact Test, P = 2.05e−4) and African elephant-specific (P = 8.30e−7) ARs than in common ARs. (d, e) Species-specific ARs disproportionately overlap DE gene regulatory regions relative to the common ARs (χ² test, P = 0.019 and P = 0.001, respectively).

Fig. 2.

Top 10 Biological Process gene ontology (GO) terms most significantly enriched with elephant accelerated genomic regions (ARs). The 10 most significantly enriched GO terms in terms of −log10(q-value) for each set of ARs (African elephant-specific, African and Asian elephant common, Asian elephant-specific), and their overlap. “Innate immune response” and “immune system process” are in the top 10 most significantly enriched GO terms for Asian elephant-specific ARs, are significantly enriched in African elephant-specific ARs but not in the top 10, and are not significantly enriched in the common ARs. “Negative regulation of T-cell proliferation” was only in the top 10 significantly enriched GO terms for the Asian elephant-specific ARs.

Fig. 3.

Evolution of TP53 in elephants and other afrotherians. (a) Phylogeny of TP53 sequences extracted from afrotherian genomes. TP53 retrogenes (Manatee RG1, eleMax, and loxAfr) appeared early in the evolution of paenungulates ∼55–60 million years ago (Ma), followed by subsequent amplification in the elephant lineage ∼45 Ma. Red dots indicate estimated nodes with posterior probability ≥90%. Red eleMax indicates TP53 retrogene sequences extracted from the “Methai” Asian elephant assembly, and blue eleMax indicates TP53 retrogene sequences extracted from the Asian elephant assembly “Icky” presented in this study. (b) TP53 copy number estimates based on read counts from three living (Asian elephant, bush, and forest elephants) and two extinct (straight-tusked elephant and woolly mammoth) elephant species. Shoulder height estimates from Larramendi (2015). Phylogeny is schematic only and represents relationships from Palkopoulou et al. (2018).