The genetic architecture of adaptations to high altitude in Ethiopia

Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control, DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.

💡 Research Summary

High‑altitude environments impose chronic hypoxia, and several human populations have lived at such elevations for millennia, suggesting genetic adaptation. While Tibetan highlanders have provided a clear model—showing strong selection on EPAS1, EGLN1, and other low‑oxygen response genes that also associate with hemoglobin (Hb) levels—the genetic basis of high‑altitude adaptation in African populations remains poorly understood. This study addressed that gap by examining two Ethiopian ethnic groups, the Amhara and the Oromo, each sampled at both high altitude (≈3,500 m) and low altitude (≈1,500 m). Genome‑wide SNP genotyping (Illumina Omni2.5‑8) and, for the Oromo, CpG methylation profiling (Illumina EPIC) were performed. Phenotypes measured were Hb concentration and arterial oxygen saturation (SpO₂).

Population structure and analysis framework
Principal‑component analysis and ADMIXTURE showed modest genetic differentiation between high‑ and low‑altitude individuals within each ethnicity, allowing the inclusion of the first three PCs as covariates in association models to control for population stratification. Linear regression was used for GWAS, adjusting for age, sex, altitude, and PCs.

Key GWAS findings

1. Hemoglobin – In the Amhara, SNP rs10803083 (located near 6q21) reached genome‑wide significance (p = 3.2 × 10⁻⁹) for association with Hb. This variant lies outside previously implicated hypoxia‑response loci and appears to be in a regulatory region of unknown function. No comparable signal was detected in the Oromo.
2. Oxygen saturation – Neither ethnic group displayed any SNPs that met genome‑wide significance for SpO₂, indicating that this trait may be governed by many small‑effect loci or by non‑genetic factors in these populations.
3. Tibetan candidate variants – The EPAS1, EGLN1, and other Tibetan‑identified variants showed no association with Hb or SpO₂ in either Ethiopian group, underscoring that high‑altitude adaptation can follow distinct genetic routes in different populations.

Allele‑frequency divergence (Fst) scan
A genome‑wide Fst comparison between high‑ and low‑altitude individuals identified no outlier loci among classic hypoxia‑response genes. Instead, the most differentiated SNPs clustered in genes involved in pathogen defense (e.g., HLA‑DRB1, KIR family) and, strikingly, in pathways governing cell‑cycle control, DNA damage response, and repair (e.g., ATM, BRCA1, CHEK2, RAD51). This pattern suggests that, beyond hypoxia, high‑altitude environments may impose selective pressures related to increased ultraviolet radiation and infection risk, favoring efficient DNA repair and immune function.

Methylation analysis
In the Oromo, differential methylation analysis between altitude groups revealed 12 CpG sites with FDR < 0.05. Affected genes included IL6, SLC2A1 (GLUT1), and VEGFA, linking epigenetic regulation of inflammation, glucose transport, and angiogenesis to altitude exposure. These findings imply that epigenetic modulation may complement genetic adaptation, fine‑tuning gene expression in response to chronic hypoxia.

Interpretation and broader implications
The absence of Tibetan‑type selection signals, together with the discovery of a novel Hb‑associated variant and the enrichment of DNA‑repair and immune pathways among highly differentiated loci, points to a fundamentally different adaptive landscape for Ethiopian highlanders. The results highlight three major themes:

• Population‑specific genetic routes – High‑altitude adaptation is not monolithic; distinct human groups can evolve unique solutions to the same physiological challenge.
• Beyond oxygen transport – While hemoglobin regulation remains important, the data suggest that protection against DNA damage and effective immune responses are also critical components of adaptation in the Ethiopian context.
• Epigenetic contribution – Altitude‑related methylation differences demonstrate that regulatory changes, possibly induced by the environment, may act alongside DNA sequence variation to shape phenotypes.

Limitations and future directions
Sample sizes (≈100–150 per subgroup) limit power to detect modest‑effect loci, especially for SpO₂. Functional validation of rs10803083 and the DNA‑repair genes identified by Fst is needed (e.g., CRISPR editing, cellular hypoxia assays). Expanding the study to include other African high‑altitude populations (e.g., Kenyan, Tanzanian) and integrating transcriptomic data would provide a more comprehensive view of convergent versus divergent adaptation mechanisms.

Conclusion
This work provides the first genome‑wide portrait of high‑altitude adaptation in Ethiopian populations. It reveals a novel hemoglobin‑associated locus, underscores the role of immune and DNA‑repair pathways, and demonstrates altitude‑linked epigenetic changes. Together, these findings broaden our understanding of human evolutionary responses to hypoxia and illustrate that different high‑altitude groups can achieve physiological resilience through diverse genetic and epigenetic strategies.