The Evolutionary Impact Of Malaria On The Saudi Arabian Genome

The sickle hemoglobin (HbS) gene has a high frequency in the Eastern Province of Saudi Arabia where it is associated with the Arab-Indian haplotype. This haplotype is characterized by HbF of 15-20% in adults and a disease phenotype that is characterized by milder anemia, splenomegaly, fewer strokes and rare leg ulcers, but with a high frequency of pain, acute chest syndrome and osteonecrosis. The emergence of malaria in Africa several millennia ago provided the selective pressure allowing the evolution of many polymorphisms that protected their carriers from the ravages of malarial infestation; the HbS gene was but one of these protective traits that emerged and reached polymorphic frequencies. The HbS gene found in our subjects from the Eastern Province might have arisen in the Indian aboriginal population of the Indus Valley Harappa culture that might be related to the pre-Arab populations of the Arabian Peninsula and distributed to the Arabian through gene flow to the Eastern Province of Saudi Arabia, Bahrain, Kuwait, and Oman.

We completed whole genome sequencing with 40x coverage on 14 unrelated individuals who were homozygous for HbS and from the indigenous population of the Al-Qatif and Al-Hasa region located along the Western shore of the Persian Gulf in the Eastern Province of the Kingdom of Saudi Arabia. Human settlement in this region dates to 3500 BC and the area was a center of trade between India and present day Iraq. This population has a little admixture with populations from other areas of the Kingdom and has inhabited the area for over 1,000 years. For each individual, there were an average of 3,282,949 SNPs, and 771,332 insertions/deletions among which we searched for variants associated with malaria resistance. Besides HbS, these patients were found to be enriched with malaria resistant variants from: DARC (Duffy Antigen), G6PD, HBA2, TIRAP, SCL4A1, CD36, FCGR2B, ABO, MARVELD3 and ATP2B4. The population has a mix of malaria resistant variants that are found in European, African and Asian populations. Among these genes are several novel variants in functionally important proteins (Table of Malaria Resistant Variants in Saudi Arabians). In CD36 which has a role in the adhesion of infected RBCs, two novel SNPs were discovered that are in functionally important sites.

Malaria has therefore been a major evolutionary force on this initial out-of-Africa population. Selective sweeps have resulted in a population with multiple protective variants and a different phenotype of sickle cell disease. Further, mitochondrial analysis of the Saudi Arabian samples found the two most frequent haplogroups were U7a and L both with frequencies of 29% each. The relative high frequency of the African ancestral L haplogroup was unexpected and suggested recent African admixture. To examine this possibility further, we performed formal tests for a history of admixture (“three population” test). This test found no evidence of admixture within the Saudi Arabian population with the African populations. The Saudi genome findings are consistent with the hypothesis that modern humans populated the Middle East 110,000 years before present, became isolated by the changing climate, and due to selective pressures of malaria, the HbS mutation and other malaria resistant variants independently arose outside of Africa.