Until recently, paleogenomic techniques were restricted to cold environments, as DNA degradation in warmer regions makes sequencing costs unaffordable. However, key chapters of human history happened in warm areas, and technical advances in capturing endogenous DNA have been developed for extending the geographic limits of ancient DNA research.
One key period of history involved the forced migration of millions of people due to slavery. Recent paleogenomic studies have helped to shed light on the origins of slaves within the trans-Atlantic trade. However, the Indian Ocean slave trade has remained understudied. In this project, we seek to elucidate the history of slavery across the Indian Ocean by focusing on Mauritius, where hundreds of thousands of slaves were imported during colonial times. We used next-generation sequencing of ancient DNA to estimate the genome-wide ancestries of individuals sampled in the historical cemetery of Le Morne (n=26), which is thought to contain the remains of Malagasy slaves. As tropical climate conditions in Mauritius are an obstacle for ancient DNA recovery, we used whole-genome in-solution capture (WISC) to enrich endogenous DNA.
Endogenous DNA accounted for 0.14–45.1% of the total. On average, through WISC we were able to increase endogenous DNA content by a factor of 13.0 (4.5–34.5), demonstrating the importance of capture-enrichment methods for paleogenomics in tropical regions. Although genome coverage was low (median=2.4%, IQR=1.1%–7.8%), for 80% of the samples, at least 2,000 SNPs intersected with a reference panel of 555 modern samples. Principal component analysis and admixture estimates indicate that samples from Le Morne had ancestries related to not only mainland Africa and Madagascar, but we also detected European and South Asian admixture. Our results represent the first genomic study to recover data from individuals involved in the Indian Ocean slave trade, and they provide insight into the complex demographic history of Mauritius.