Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

Schroeder, Hannes; Ávila-Arcos, María C.; Malaspinas, Anna-Sapfo; Poznik, G. David; Sandoval-Velasco, Marcela; Carpenter, Meredith L.; Moreno-Mayar, J. Víctor; Sikora, Martin; Johnson, Philip L.; Allentoft, Morten E.; Samaniego, José A.; Haviser, Jay B.; Dee, Michael W.; Stafford, Thomas W.; Salas, Antonio; Orlando, Ludovic; Willerslev, Eske; Bustamante, Carlos D.; Gilbert, M. Thomas P.

doi:10.1073/pnas.1421784112

Cited by 105 publications

(116 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Adding assortment and migrations, we find that the estimated number of generations since the admixture event is 15. Assuming a generation time of 25 years, this places the initial migrations in the mid-17th century, which is consistent with the history of African Americans (Schroeder et al 2015). …”

supporting

confidence: 81%

The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium

Zaitlen

Huntsman

et al. 2017

Genetics

View full text Add to dashboard Cite

Statistical models in medical and population genetics typically assume that individuals assort randomly in a population. While this simplifies model complexity, it contradicts an increasing body of evidence of nonrandom mating in human populations. Specifically, it has been shown that assortative mating is significantly affected by genomic ancestry. In this work, we examine the effects of ancestry-assortative mating on the linkage disequilibrium between local ancestry tracks of individuals in an admixed population. To accomplish this, we develop an extension to the Wright-Fisher model that allows for ancestry-based assortative mating. We show that ancestry-assortment perturbs the distribution of local ancestry linkage disequilibrium (LAD) and the variance of ancestry in a population as a function of the number of generations since admixture. This assortment effect can induce errors in demographic inference of admixed populations when methods assume random mating. We derive closed form formulae for LAD under an assortative-mating model with and without migration. We observe that LAD depends on the correlation of global ancestry of couples in each generation, the migration rate of each of the ancestral populations, the initial proportions of ancestral populations, and the number of generations since admixture. We also present the first direct evidence of ancestry-assortment in African Americans and examine LAD in simulated and real admixed population data of African Americans. We find that demographic inference under the assumption of random mating significantly underestimates the number of generations since admixture, and that accounting for assortative mating using the patterns of LAD results in estimates that more closely agrees with the historical narrative.

show abstract

supporting

confidence: 81%

The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium

Zaitlen

Huntsman

et al. 2017

Genetics

View full text Add to dashboard Cite

show abstract

“…This is consistent with slave records and previous genome-wide analyses of African Americans indicating that most sharing occurred in West and West-Central Africa. [80][81][82] There are subtle differences between the African origins of the ACB and ASW populations (e.g., difference in distance from YRI on AS-PC1 and AS-PC2 p ¼ 6.4 3 10 À6 ), likely due either to mild island founder effects in the ACB samples or differences in African source populations for enslaved Africans who remained in Barbados versus those who were brought to the USA. The Native tracts of ancestry from the AMR populations first separate the southernmost PEL populations from the CLM, MXL, and PUR on AS-PC1, then separate the northernmost MXL from the CLM and PUR on AS-PC2, consistent with a north-south cline of divergence among indigenous Native American ancestry ( Figure 1G).…”

Section: Genetic Diversity Within and Between Populations In The Amermentioning

confidence: 99%

Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations

Gignoux

Walters

et al. 2017

The American Journal of Human Genetics

Self Cite

1,244

1,153

View full text Add to dashboard Cite

The vast majority of genome-wide association studies (GWASs) are performed in Europeans, and their transferability to other populations is dependent on many factors (e.g., linkage disequilibrium, allele frequencies, genetic architecture). As medical genomics studies become increasingly large and diverse, gaining insights into population history and consequently the transferability of disease risk measurement is critical. Here, we disentangle recent population history in the widely used 1000 Genomes Project reference panel, with an emphasis on populations underrepresented in medical studies. To examine the transferability of single-ancestry GWASs, we used published summary statistics to calculate polygenic risk scores for eight well-studied phenotypes. We identify directional inconsistencies in all scores; for example, height is predicted to decrease with genetic distance from Europeans, despite robust anthropological evidence that West Africans are as tall as Europeans on average. To gain deeper quantitative insights into GWAS transferability, we developed a complex trait coalescent-based simulation framework considering effects of polygenicity, causal allele frequency divergence, and heritability. As expected, correlations between true and inferred risk are typically highest in the population from which summary statistics were derived. We demonstrate that scores inferred from European GWASs are biased by genetic drift in other populations even when choosing the same causal variants and that biases in any direction are possible and unpredictable. This work cautions that summarizing findings from large-scale GWASs may have limited portability to other populations using standard approaches and highlights the need for generalized risk prediction methods and the inclusion of more diverse individuals in medical genomics.

show abstract

mentioning

confidence: 99%

“…17) and have been used to assign historic individuals to their most likely geographic origin (18)(19)(20). In particular, the genome-wide analysis of 1,000s or more single nucleotide polymorphisms (SNPs) allows the determination of an individual's geographic origin with accuracy and precision, even when limited genetic differentiation exists among regions (20)(21)(22). Since low levels of genetic differentiation are typical for marine species with high dispersal capabilities like Atlantic cod (23,24), such genome-wide approaches are essential to increase the assignment power of modern (22) and ancient samples of these species (25).…”

mentioning

confidence: 99%

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

Star

Boessenkool

Gondek

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

115

View full text Add to dashboard Cite

Knowledge of the range and chronology of historic trade and long-distance transport of natural resources is essential for determining the impacts of past human activities on marine environments. However, the specific biological sources of imported fauna are often difficult to identify, in particular if species have a wide spatial distribution and lack clear osteological or isotopic differentiation between populations. Here, we report that ancient fishbone remains, despite being porous, brittle, and light, provide an excellent source of endogenous DNA (15-46%) of sufficient quality for whole-genome reconstruction. By comparing ancient sequence data to that of modern specimens, we determine the biological origin of 15 Viking Age (800-1066 CE) and subsequent medieval (1066-1280 CE) Atlantic cod (Gadus morhua) specimens from excavation sites in Germany, Norway, and the United Kingdom. Archaeological context indicates that one of these sites was a fishing settlement for the procurement of local catches, whereas the other localities were centers of trade. Fish from the trade sites show a mixed ancestry and are statistically differentiated from local fish populations. Moreover, Viking Age samples from Haithabu, Germany, are traced back to the North East Arctic Atlantic cod population that has supported the Lofoten fisheries of Norway for centuries. Our results resolve a long-standing controversial hypothesis and indicate that the marine resources of the North Atlantic Ocean were used to sustain an international demand for protein as far back as the Viking Age.genomics | high-throughput sequencing | trade | chromosomal inversion | fish bone

show abstract

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

Cited by 105 publications

References 38 publications

The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium

The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium

Human Demographic History Impacts Genetic Risk Prediction across Diverse Populations

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

Contact Info

Product

Resources

About