Genomic Ancestry of Saint Helena’s Liberated Africans

Historians have long been interested in the origins of the millions of enslaved Africans who were transported to the Americas, but there is little direct evidence to go on (1, 2). Although much is known about the volume and changing demographic trends of the Atlantic slave trade, the African origins of the enslaved remain largely unknown (3). Genome-wide analyses of SNPs provide a powerful tool for estimating individual ancestry, and several studies (e.g., refs. 4 and 5) have shown that they can be used to infer an individual’s geographic origin with great accuracy. In the present study, we used genome-wide data to trace the origins of three enslaved Africans whose remains were recovered in the Zoutsteeg area of Philipsburg on the Caribbean island of Saint Martin (Materials and Methods). Previous reports (6) suggest that the “Zoutsteeg Three,” as they became known locally, were likely born in Africa as opposed to the New World. But they did not reveal where in Africa they originated.

Bayesian analysis of individual calibrated radiocarbon dates suggests that the burials date between A.D. 1660 and 1688 (for more details, see SI Appendix, Section 2). During this period, Saint Martin—like other islands—relied to a large extent on African slave labor, but there are no records about the slaves’ origins in Africa. The Transatlantic Slave Trade Database (slavevoyages.org), a large online repository containing information on over 35,000 slaving voyages, lists only a single vessel that arrived in Saint Martin between A.D. 1650 and 1700, although there were undoubtedly more for which there are no records. Moreover, the lone entry does not give the African port of embarkation or any information on the slave cargo. Given the lack of documentation, we embarked on a genomic study with the goal of identifying the genetic origins of the Zoutsteeg Three in Africa.


Table 1.
Modeled radiocarbon dates and sequencing results for the Zoutsteeg Three

Sample Modeled 14C age* Sex† Nuclear coverage Contamination (%)‡ Damage (%)§ Mt coverage Mt haplogroup Y haplogroup
STM1 A.D. 1660–1688 M 0.3× 0.63 16.8 641× L3b1a R1b1c-V88
STM2 A.D. 1660–1688 M 0.1× 0.22 23.2 543× L3d1b —
STM3 A.D. 1660–1688 F 0.5× 0.15 14.9 651× L2a1f —
↵* Modeled age range of the samples based on Bayesian analysis of individual calibrated radiocarbon dates.

↵† Biological sex inferred from the ratio of reads mapping to X and Y chromosomes (44).

↵‡ Likelihood-based contamination estimate based on mtDNA reads (10).

↵§ Frequency of C-to-T misincorporations at 5' ends of sequencing reads.


Results
Initial shotgun sequencing revealed that the DNA in the samples was very poorly preserved (SI Appendix, Section 8). This result was expected because DNA preservation in the Caribbean is known to be poor (7). The fraction of nonredundant reads mapping to the human reference genome varied between 0.3% and 7.6%, and the sequences showed all features typical of ancient DNA, including short average read lengths (∼67 bp), characteristic fragmentation patterns, and an increased frequency of apparent C-to-T substitutions toward the 5′ ends of molecules (see Table 1 and SI Appendix, Fig. S7). To increase sequencing efficiency and lower cost, we enriched the ancient DNA libraries using two recently developed whole-genome capture methods (8, 9). Following enrichment, we generated between 0.1- and 0.5-fold genome-wide coverage for the three individuals, which proved to be sufficient to infer their likely origins within Africa.

Although the presence of characteristic damage patterns and short average read lengths suggest that authentic ancient molecules were sequenced, it is possible that some degree of modern contamination could be present in the data. Therefore, we used a previously published Bayesian method (10) to detect contamination and found very low (i.e., <1%) levels overall (see Table 1 and SI Appendix, Section 9). We then merged our ancient sequence data with genotype data from the Human Genome Diversity Cell Line Panel (HGDP) reference panel (11) and used principal component analysis (PCA) (12) to confirm the individuals’ African ancestry (for more details, see SI Appendix, Section 12). Because of low depth, we randomly sampled a single allele from both ancient and modern individuals, as done in ref. 13. As expected, all three individuals fell within African variation as defined by PC1 and PC2 (SI Appendix, Fig. S17). This clustering was retained upon restricting the analysis to sequences showing signs of ancient DNA damage (14) (SI Appendix, Fig. S18), indicating that the signal was not driven by modern DNA contamination.


Fig. 1.
Genetic affinities of the Zoutsteeg individuals. (A) D-statistic test results for STM3. Error bars correspond to 3 SEs of the D-statistic. Results for STM1 and STM2 are plotted in SI Appendix, Fig. S18. (B) Sampling locations for the 11 African populations in our reference panel (17). (C) Procrustes-transformed PCA plot of the Zoutsteeg individuals with African reference panel samples. (D) Ancestry proportions for the Zoutsteeg individuals and those of 188 African individuals in the reference panel, as inferred by ADMIXTURE analysis (19)

D-Statistic Test.
We then tested the relationships between each sample (henceforth referred to as STM1, STM2, and STM3) and 11 populations from across the world for which whole genome data were available (15), using a D-test of the form D (chimpanzee, STM; Yoruba, X), where X stands for a population other than Yoruba (for more details, see SI Appendix, Section 13). We found that the STMs were significantly more closely related to the Yoruba than to any non-African population (Fig. 1A), again confirming their African origins. Within Africa, the STMs appeared significantly more closely related to the Yoruba than to hunter-gatherer populations (San, Mbuti Pygmies). This was not surprising, as the San and the Mbuti were not represented in the transatlantic slave trade. For the Mandenka and Dinka, the D-test results were not significant, suggesting that these populations are equally closely related to the STMs as are the Yoruba. The lack of rejection for the Dinka was surprising, as this population—from southern Sudan—is not known to have been involved in the Atlantic slave trade (16).