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. 2021 Aug;175(4):905-919.
doi: 10.1002/ajpa.24333. Epub 2021 May 19.

Genetic landscape of Gullah African Americans

Kip D Zimmerman  1 , Theodore G Schurr  2 , Wei-Min Chen  3   4 , Uma Nayak  3 , Josyf C Mychaleckyj  3   4 , Queen Quet  5 , Lee H Moultrie  6 , Jasmin Divers  7 , Keith L Keene  8   9 , Diane L Kamen  10 , Gary S Gilkeson  10 , Kelly J Hunt  11 , Ida J Spruill  12 , Jyotika K Fernandes  10 , Melinda C Aldrich  13   14   15   16 , David Reich  17   18   19   20 , W Timothy Garvey  21 , Carl D Langefeld  1 , Michèle M Sale  3   4 , Paula S Ramos  10   11
Affiliations

Genetic landscape of Gullah African Americans

Kip D Zimmerman et al. Am J Phys Anthropol. 2021 Aug.

Abstract

Objectives: Gullah African Americans are descendants of formerly enslaved Africans living in the Sea Islands along the coast of the southeastern U.S., from North Carolina to Florida. Their relatively high numbers and geographic isolation were conducive to the development and preservation of a unique culture that retains deep African features. Although historical evidence supports a West-Central African ancestry for the Gullah, linguistic and cultural evidence of a connection to Sierra Leone has led to the suggestion of this country/region as their ancestral home. This study sought to elucidate the genetic structure and ancestry of the Gullah.

Materials and methods: We leveraged whole-genome genotype data from Gullah, African Americans from Jackson, Mississippi, African populations from Sierra Leone, and population reference panels from Africa and Europe to infer population structure, ancestry proportions, and global estimates of admixture.

Results: Relative to non-Gullah African Americans from the Southeast US, the Gullah exhibited higher mean African ancestry, lower European admixture, a similarly small Native American contribution, and increased male-biased European admixture. A slightly tighter bottleneck in the Gullah 13 generations ago suggests a largely shared demographic history with non-Gullah African Americans. Despite a slightly higher relatedness to populations from Sierra Leone, our data demonstrate that the Gullah are genetically related to many West African populations.

Discussion: This study confirms that subtle differences in African American population structure exist at finer regional levels. Such observations can help to inform medical genetics research in African Americans, and guide the interpretation of genetic data used by African Americans seeking to explore ancestral identities.

Keywords: West Africa; admixture; ancestry; demography; slavery.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

FIGURE 1
FIGURE 1
Principal component analysis of all African samples. Principal component analysis (PCA) (EIGENSOFT) was applied to HGDP and HapMap III African and Sierra Leonean populations. (a) PCA showing the Mozabite cluster (along PC1), the West, Eastern and Southern, and Middle and South Western subpopulations clusters (along PC2). Insert shows approximate locations of sampled populations in Africa. (b) PCA of Sierra Leone ethnic groups with n > 10 showing the Mende, Creole and Temne forming relatively different, but overlapping, clusters
FIGURE 2
FIGURE 2
Ancestry estimates for European, African, and African American populations. ADMIXTURE analysis in Europeans, Africans (including Sierra Leone ethnic groups) and African Americans, assuming two through five ancestral genetic clusters (k = 2 through k = 5). The k = 5 setting has the lowest cross‐validation error of k = 2–8. Populations were ordered via hierarchical cluster analysis. The plot shows each individual as a thin vertical column colored in proportion to their estimated ancestry from one particular population. The initial distinction is between Europeans (blue) and Africans (other colors). Within Africans, red indicates a West African (aka African Rice Coast) ancestry (highest in the Mandenka of Senegal and Sierra Leone ethnic groups), orange a Central and South African ancestry (highest in the San of Namibia and Mbuti of Democratic Republic of the Congo), yellow an East African ancestry (highest in Maasai and Luhya of Kenya), and green a West‐Central African ancestry (aka Bight of Benin) ancestry (highest in the Yoruba of Nigeria)
FIGURE 3
FIGURE 3
Principal component analysis of Gullah and non‐Gullah African Americans. (a) Principal component analysis (EIGENSOFT) using European (CEU samples from Utah) and African ancestral reference populations (YRI samples from Nigeria, Mandenka from Senegal, and Sierra Leone samples) illustrates the Gullah's closeness to Sierra Leone populations and the Mandenka, and also non‐Gullah (JHS) African Americans' proximity to the Yoruba. (b) To demonstrate the difference between Gullah and JHS African Americans, a PerMANOVA analysis was computed for each set of principal components between PC1 and PC6 to test for differences between the two groups; the resulting analyses each demonstrated significant differences (1 × 10−3), indicating a significant distance between the two groups. (c) Comparisons of each individual principal component between the Gullah and JHS. Wilcoxon p‐values are displayed. PC1 and PC2 appear to be the primary drivers in the differences between the Gullah and JHS. AA: African American; JHS: Jackson Heart Study African Americans from Jackson, Mississippi
FIGURE 4
FIGURE 4
Estimation of ancestry‐specific recent effective population size from segments of identity by descent (IBD) in Gullah and JHS African Americans. Plot displays the recent effective population size (Ne) in Gullah and JHS African Americans over the past 50 generations. The lines show the estimated effective population size based on IBD segments associated only with African ancestry, while the colored regions show 95% bootstrap confidence intervals. The graph displays a bottleneck event occurring nearly 13 generations ago, an estimate consistent with the turn of the 18th century. We used the ancestry‐specific IBDNe pipeline to estimate the effective population sizes
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