Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs

Yahya M Khubrani,Jon H Wetton,Mark A Jobling

doi:10.1016/j.fsigen.2017.11.015

Yahya M Khubrani, Jon H Wetton + Show 1 more

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https://doi.org/10.1016/j.fsigen.2017.11.015

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Abstract

Saudi Arabia’s indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler® set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for Saudi Arabia generally, and caution is needed when considering expatriate groups as representative of country of origin. Our study shows the importance of geographical and social structuring that may affect the utility of forensic databases and the interpretation of Y-STR profiles.

Highlights

Saudi Arabia is the largest country in the Arabian Peninsula
In another mitochondrial DNA (mtDNA)-based study [5] - the only example to divide Saudi Arabia sub-regionally - central, northern, western and southeastern sub-groups formed a single cluster in a multi-dimensional scaling (MDS) analysis when compared to other Arabian Peninsula samples, and presented significant inter-group differences
The second study [7] showed that haplogroup J1 was the most prominent lineage (42%) in the Saudi Arabian sample studied, and that genetic distances based on haplogroup frequencies were relatively small among Arabian Peninsula samples

Summary

Introduction

Saudi Arabia is the largest country in the Arabian Peninsula. Its population of ~32 million people is distributed highly non-uniformly (Figure 1), with very low densities in its large desert areas, but high densities concentrated around a small number of cities. Its indigenous Arab people (~63% of the population; www.stats.gov.sa, accessed 12/07/17) are historically organized into geographically-differentiated patrilineal descent groups, or tribes [1], with a tradition of consanguinity [2] This geographical and social organization might be expected to have an effect on patterns of genetic diversity, regarding the male-specific region of the Y chromosome (MSY), which in turn could have implications in interpretation of DNA profiles. Ychromosome studies have analysed the seven Y-STRs defining the minimal haplotype [6], or haplogroup-defining SNPs together with 17 Y-STRs (Yfiler®) for one specific haplogroup [7] The first of these [6] revealed lower diversity in Saudi Arabia than in populations from outside the Arabian Peninsula, and affinity between Saudi Arabia and Yemen, which together were strongly differentiated from Oman and Dubai. We compare the spectrum of Y-chromosome types in males recruited within Saudi Arabia with that of regionally-matched males recruited in the United Kingdom, to ask if social structuring influences patterns of Y-haplotype diversity

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