Reconstructing an African haploid genome from the 18th century

Jagadeesan, Anuradha; Gunnarsdóttir, Ellen; Ebenesersdóttir, S. Sunna; Guðmundsdóttir, Valdís B.; Þórðardóttir, Elísabet Linda; Einarsdóttir, Margrét; Dugoujon, Jean‐Michel; Fortes-Lima, César; Migot-Nabias, Florence; Massougbodji, Achille; Bellis, Gil; Pereira, Luı́sa; Másson, Gísli; Kong, Augustine; Stefánsson, Kāri; Helgason, Agnar

doi:10.1038/s41588-017-0031-6

Cited by 18 publications

(17 citation statements)

References 37 publications

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“…To get a more direct handle on the genetic affinities of the African individuals and their origins, we computed a weighted measure of genomic identity by state (wIBS) (21) between each individual in our dataset and 841 individuals from 22 present-day reference populations from West Central Africa (7). Higher wIBS scores indicate stronger genetic affinity between the historical individual and any given reference population.…”

Section: Diverse Origins In West Central Africamentioning

confidence: 99%

“…Weighted IBS. To estimate the affinity of the studied individuals to possible African source populations, we performed an analysis based on a pairwise identity-by-state weighted by allele frequencies (wIBS) (21) in the West Central Africa panel where sample sizes were greater than nine. In order to test whether the reference population with the greatest mean wIBS for each of the individuals (refwIBS) was significantly greater than the value observed for other reference populations, we performed population pairwise permutation tests.…”

Section: Admixture Analysismentioning

confidence: 99%

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The genetic origins of Saint Helena’s liberated Africans

Sandoval-Velasco

Jagadeesan

Ávila‐Arcos

et al. 2019

Preprint

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Between the early 16 th and late 19 th centuries, an estimated 12 million Africans were transported to the Americas as part of the transatlantic slave trade. Following Britain's abolition of slave trade in 1807, the Royal Navy patrolled the Atlantic and intercepted slave ships that continued to operate. During this period, the island of St Helena in the middle of the South Atlantic served as a depot for "liberated" Africans. Between 1840 and 1867, approximately 27,000 Africans were disembarked on the island. To investigate their origins, we generated genome-wide ancient DNA data for 20 individuals recovered from St Helena. The genetic data indicate that they came from West Central Africa, possibly the area of present-day Gabon and Angola. The data further suggest that they did not belong to a single population, confirming historical reports of cultural heterogeneity among the island's African community. Our results shed new light on the origins of enslaved Africans during the final stages of the slave trade and illustrate how genetic data can be used to complement and validate existing historical sources.

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Section: Diverse Origins In West Central Africamentioning

confidence: 99%

Section: Admixture Analysismentioning

confidence: 99%

The genetic origins of Saint Helena’s liberated Africans

Sandoval-Velasco

Jagadeesan

Ávila‐Arcos

et al. 2019

Preprint

Self Cite

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“…As such, the primacy and appeal of DNA ancestry tests that reproduce a particular North American model of identity, prizing the recuperation of "ethnic" labels as a means of symbolically "reversing the Middle Passage," should not be taken as universal, nor should this paradigm be placed above alternative ways of thinking and commemorating slave-descent that have developed out of different historical, cultural, and political contexts. Neither should DNA "ethnicity" analyses be regarded as the only tool that genetics can contribute towards researching the lives and identities of enslaved Africans-as emerging studies from other Atlantic contexts are beginning to show (e.g., Callaway 2016;Jagadeesan et al 2018;Pálsson 2016, pp. 228-29).…”

Section: Discussionmentioning

confidence: 99%

Of African Descent? Blackness and the Concept of Origins in Cultural Perspective

Abel

2018

Genealogy

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Over the past decade, the DNA ancestry-testing industry-based largely in the United States-has experienced a huge upsurge in popularity, thanks partly to rapidly developing technologies and the falling prices of products. Meanwhile, the notion of "genetic genealogy" has been strongly endorsed by popular television documentary shows in the US, particularly vis-à-vis African-American roots-seekers-for whom these products are offered as a means to discover one's ancestral "ethnic" origins, thereby "reversing the Middle Passage." Yet personalized DNA ancestry tests have not had the same reception among people of African descent in other societies that were historically affected by slavery. This paper outlines and contextualizes these divergent responses by examining and comparing the cultural and political meanings that are attached to notions of origin, as well as the way that Blackness has been defined and articulated, in three different settings: the United States, France and Brazil.

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“…However, their pedigree was much smaller (with no loops), many fewer markers (450) were used, and several of the reconstruction steps were done by inspection or by hand, which does not scale to our scenario. Another study [22] reconstructed the African haplotype of an African-European individual who migrated to Iceland in 1802 and had 788 descendants, 182 of which were genotyped. However, this scenario is much simpler, as the regions of African ancestry within each descendant were easily identified and all belonged to the same individual.…”

Section: Introductionmentioning

confidence: 99%

Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent

Finke

Kourakos

Brown

et al. 2020

Preprint

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In this work we develop a novel algorithm for reconstructing the genomes of ancestral individuals, given genotype or sequence data from contemporary individuals and an extended pedigree of family relationships. A pedigree with complete genomes for every individual enables the study of allele frequency dynamics and haplotype diversity across generations, including deviations from neutrality such as transmission distortion. When studying heritable diseases, ancestral haplotypes can be used to augment genome-wide association studies or compute polygenic risk scores for the reconstructed individuals.The building blocks of our reconstruction algorithm are segments of Identity-By-Descent (IBD) shared between two or more genotyped individuals. The method alternates between finding a source for each IBD segment and assembling IBD segments placed within each ancestral individual. After each iteration we perform conflict resolution to remove IBD segments that do not align with wellreconstructed haplotypes and upweight the probability that these segments should be placed in other individuals. We repeat this process until we are no longer successfully reconstructing additional ancestral haplotypes. Unlike previous approaches, our method is able to accommodate complex pedigree structures with hundreds of individuals genotyped at millions of SNPs.We apply our method to an Old Order Amish pedigree from Lancaster, Pennsylvania, whose founders came to the United States from Europe during the early 18th century. The pedigree includes 1338 individuals from the past 10 generations, 394 with genotype data. The motivation for reconstruction is to understand the genetic basis of diseases segregating in the family through tracking haplotype transmission over time. Using our algorithm thread, we are able to reconstruct an average of 230 ancestral individuals per autosome. thread was developed for endogamous populations, but can be applied to any extensive pedigree with the recent generations genotyped. We anticipate that this type of practical ancestral reconstruction will become more common and necessary to understand rare and complex heritable diseases in extended families.

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Reconstructing an African haploid genome from the 18th century

Cited by 18 publications

References 37 publications

The genetic origins of Saint Helena’s liberated Africans

The genetic origins of Saint Helena’s liberated Africans

Of African Descent? Blackness and the Concept of Origins in Cultural Perspective

Ancestral Haplotype Reconstruction in Endogamous Populations using Identity-By-Descent

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