Genetic ancestry, admixture, and population structure in rural Dominica

• Published in: PloS one 2021-11, Vol.16 (11), p.e0258735-e0258735
• Main Authors: Keith, Monica H, Flinn, Mark V, Durbin, Harly J, Rowan, Troy N, Blomquist, Gregory E, Taylor, Kristen H, Taylor, Jeremy F, Decker, Jared E
• Format: Article
• Language: English
• Subjects: 18th century; Admixtures; Adolescent; Adult; Algorithms; Analysis; Animal sciences; Biology and Life Sciences; Blacks - genetics; Clustering; Decay; Dominica - epidemiology; Earth Sciences; Ecological effects; Ecology and Environmental Sciences; Ethnicity - genetics; Female; Gene polymorphism; Genealogy; Genetic analysis; Genetic diversity; Genetic research; Genetic structure; Genetic Variation - genetics; Genetics, Population; Genome, Human - genetics; Genomes; Genotype & phenotype; Hispanic or Latino - genetics; Historical structures; Horticulture; Humans; Linkage disequilibrium; Linkage Disequilibrium - genetics; Male; Middle Aged; Mitochondria; Nucleotides; People and places; Polymorphism; Polymorphism, Single Nucleotide - genetics; Population; Population biology; Population genetics; Population structure; Population studies; Postcolonialism; Rural Population; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Vegetation; Violence; West Indies - epidemiology; Whites - genetics; Young Adult
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0258735

The Caribbean is a genetically diverse region with heterogeneous admixture compositions influenced by local island ecologies, migrations, colonial conflicts, and demographic histories. The Commonwealth of Dominica is a mountainous island in the Lesser Antilles historically known to harbor communities with unique patterns of migration, mixture, and isolation. This community-based population genetic study adds biological evidence to inform post-colonial narrative histories in a Dominican horticultural village. High density single nucleotide polymorphism data paired with a previously compiled genealogy provide the first genome-wide insights on genetic ancestry and population structure in Dominica. We assessed family-based clustering, inferred global ancestry, and dated recent admixture by implementing the fastSTRUCTURE clustering algorithm, modeling graph-based migration with TreeMix, assessing patterns of linkage disequilibrium decay with ALDER, and visualizing data from Dominica with Human Genome Diversity Panel references. These analyses distinguish family-based genetic structure from variation in African, European, and indigenous Amerindian admixture proportions, and analyses of linkage disequilibrium decay estimate admixture dates 5-6 generations (~160 years) ago. African ancestry accounts for the largest mixture components, followed by European and then indigenous components; however, our global ancestry inferences are consistent with previous mitochondrial, Y chromosome, and ancestry marker data from Dominica that show uniquely higher proportions of indigenous ancestry and lower proportions of African ancestry relative to known admixture in other French- and English-speaking Caribbean islands. Our genetic results support local narratives about the community's history and founding, which indicate that newly emancipated people settled in the steep, dense vegetation along Dominica's eastern coast in the mid-19th century. Strong genetic signals of post-colonial admixture and family-based structure highlight the localized impacts of colonial forces and island ecologies in this region, and more data from other groups are needed to more broadly inform on Dominica's complex history and present diversity.