pubmed.ncbi.nlm.nih.gov

Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia - PubMed

Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia

Kendra Sirak et al. Nat Ecol Evol. 2024 Apr.

Abstract

Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between Africa and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travellers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. Here we report genome-wide data from 39 individuals who lived between ~650 and 1750 CE at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modelled as deriving ~86% of their ancestry from a population such as that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups such as Late Pleistocene hunter-gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harboured a small population that showed qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.

© 2024. The Author(s), under exclusive licence to Springer Nature Limited.

PubMed Disclaimer

Conflict of interest statement

COMPETING INTEREST STATEMENT

The authors declare no competing interests.

Figures

Extended Data Figure 1.
Extended Data Figure 1.. Heatmap of pairwise qpWave tests for 32 medieval Soqotri individuals with sufficient SNP coverage.

Data are in Supplementary Data 4 and details are in Supplementary Note 5. We interpret pairwise model p-values >0.01 (colored cells) to be consistent with the two individuals forming a clade relative to the reference population set, and p-values <0.01 (grey cells) to be inconsistent.

Figure 1.
Figure 1.. Overview of Soqotri burials with analysis of shared drift between medieval Soqotri and present-day groups.

(A) Location of Soqotra. The Soqotra archipelago, situated at the crossroads of Arabia and Africa, is identified by the black box. (B) On the left, the 250 highest outgroup f3-statistics show shared drift between the medieval Soqotri and present-day populations genotyped on the Affymetrix Human Origins (HO) array using Karitiana as an outgroup. The color scale is in the bottom left corner, showing highest amount of allele sharing with the Yemeni_Desert group. Data are in Supplementary Data 8 and additional details about outgroup f3-statistic analysis are in Supplementary Note 7. (C) Burial patterns by sex and genetic relationships across 15 tafoni (A-O) on Soqotra. Legend is in the bottom left corner with additional information in Supplementary Data 14 and Supplementary Note 10. A timeline of tafone usage based on direct 14C dates and dates of lineal relatives with known relationships is included (bottom center).

Figure 2.
Figure 2.. Qualitative analyses of medieval Soqotri DNA.

(A) PCA. We computed axes with present-day individuals (Supplementary Note 4) and projected ancient individuals onto PCs 1 and 2. Inset provides a zoomed view of the Soqotri cluster. (B) Unsupervised ADMIXTURE at K=10 components for 39 Soqotri individuals. Individuals with <15,000 SNPs are marked “_lc” denoting low coverage; we include calibrated dates when available. Individuals are grouped by site starting on the northeast of the island and moving clockwise (site name written next to the plot), then by burial tafone (labeled A – O), see Supplementary Data 14). Members of four families are identified (Fam 1 – Fam 4, see Supplementary Data 13). (C) Additional results of unsupervised ADMIXTURE at K=10 components. Data for the Soqotri and relevant present-day groups from Egypt and the Near East are on top. The Soqotri are in the same order as in Panel B (top to bottom in Panel B corresponding to right to left in Panel C), with low coverage individuals denoted with a cross symbol and the outlier by an asterisk. A reference panel for the 10 components is on the bottom.

Figure 3.
Figure 3.. Medieval Soqotri had fewer long ROH than expected from modern ethnographic studies.

We focused on long ROH (>20cM) as it is unlikely to arise except for unions of people in the same extended family, and hence inferences based on it are relatively unaffected by artifacts due to small island population sizes. (A) 1000 simulations of individual ROH profiles. We compare the real data to 1000 simulations of people whose parents are first cousins, under the simplifying assumption that all other genealogical relationships between peoples’ parents are very deep in the past. Treated as a single hypothesis test, I20705 (who has the most ROH out of the 14 ancient individuals for which we had ROH results) is in the p=0.26 percentile (one-sided test) of simulations with respect to the total summed ROH>20cM, and the p=0.29 percentile (one-sided test) of simulations with respect to the largest ROH segment. While this is in the range expected for the product of a first cousin union when treated as a single hypothesis test, it is surprisingly low given that modern ethnographic rates would predict about five first cousin unions in the data. (B) 1000 simulated sets of 14 individuals. We compare the maximum ROH observed in 1000 simulations of 14 individuals assuming the modern ethnographic rate of 40% first cousin unions and find that the real data is at the p=0.007 percentile (one-sided test) of simulations with respect to the total summed ROH>20cM, and p=0.009 percentile (one-sided test) of simulations with respect to largest ROH segment.

Similar articles

References

    1. Agranat-Tamir L, Waldman S, Martin MAS, Gokhman D, Mishol N, Eshel T, Cheronet O, Rohland N, Mallick S, Adamski N, Lawson AM, Mah M, Michel M, Oppenheimer J, Stewardson K, Candilio F, Keating D, Gamarra B, Tzur S, … Reich D (2020). The Genomic History of the Bronze Age Southern Levant. Cell, 181(5), 1146–1157. - PMC - PubMed
    1. Al-Abri A, Podgorná E, Rose JI, Pereira L, Mulligan CJ, Silva NM, Bayoumi R, Soares P, & Černý V Pleistocene-Holocene boundary in Southern Aabia from the perspective of human mtDNA variation. (2012). American Journal of Physical Anthropology, 149, 21–28. - PubMed
    1. Al-Mujāwir I, & ibn Yaʿqūb Y (2008). A traveller in thirteenth-century Arabia: Ibn al-Mujāwir’s Tārīkh almustabṣir. Ashgate.
    1. Alexander DH, Novembre J, & Lange K (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19(9), 1655–1664. - PMC - PubMed
    1. Almarri MA, Haber M, Lootah RA, Hallast P, Al Turki S, Martin HC, Xue Y, & Tyler-Smith C (2021). The genomic history of the Middle East. Cell, 184(18), 4612–4625. e4614. - PMC - PubMed

MeSH terms

Substances