Genetic ancestry, admixture, and population structure in rural Dominica

Abstract

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.

Native American Ancestry and Pigmentation Allele Contributions to Skin Color in a Caribbean Population

“…The 55% Native American ancestry calculated from autosomal genotype in the Kalinago is greater than the reported 13% in Puerto Rico (Gravel et al, 2013), 10-15% for Tainos across the Caribbean (Schroeder et al, 2018), and 8% for Cubans (Marcheco-Teruel et al, 2014). This is also considerably higher than the reported 6% Native American ancestry found in Bwa Mawego, a horticultural population that resides south of the Kalinago Territory (Keith et al, 2021). However, this result is lower than the 67% Native American ancestry reported by Crawford et al (2021) for an independently collected Kalinago samples based on the mtDNA haplotype analysis.…”

“…This would have increased the frequency of novel dark skin variants, if any, and would have decreased the frequency of light skin variants that had not achieved fixation. Hypopigmenting alleles are associated with the European admixture characteristic of many current Native American populations (Brown et al, 2017;Gravel et al, 2013;Keith et al, 2021;Klimentidis et al, 2009;Reich et al, 2012).…”

“…This would have increased the frequency of novel dark skin variants, if any, and would have decreased the frequency of light skin variants that had not achieved fixation. Hypopigmenting alleles are associated with the European admixture characteristic of many current Native American populations (Brown et al, 2017; Gravel et al, 2013; Keith et al, 2021; Klimentidis et al, 2009; Reich et al, 2012). Since the European hypopigmenting alleles may mask the effects of East Asian and Native American alleles, we searched for an admixed Native American population with high African, but low European admixture.…”

Anthropological genetic insights on Caribbean population history

“…11,80 Over the last two decades, research into Caribbean post-contact population history has largely focused on investigating the impact of historical migrations on extant patterns of genetic structure and admixture. Most of these studies can be broadly classified into four, sometimes overlapping, research categories: (1) Local histories focusing on one or more island communities and often seeking to characterize the impact of local sociocultural and historical processes on biocultural diversity, 9,10,[38][39][40]43,45,49,50,60,65,75,77,[81][82][83][84][85][86][87][88] (2) Regional histories surveying broad patterns of genetic diversity across several islands which are usually grouped together due to some unifying geographic, historical or linguistic factor (e.g., the Lesser Antilles, the former French colonies, the Anglophone islands), 11,[46][47][48]74,76,89 (3) Large scale surveys or metanalyses of genomic variation in the Americas that include island or diasporic Caribbean populations, 12,80,90,91 and (4) Biomedical or evolutionary genetic studies investigating the impact of population history on human health and phenotypic diversity. 41,92,93 Although all of these studies characterize overall patterns of genetic structure, ancestry and admixture, some of them also focus on specific questions such as tracing subcontinental ancestries,...…”

Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population

“…This would have increased the frequency of novel dark skin variants, if any, and would have decreased the frequency of light skin variants that had not achieved fixation. Hypopigmenting alleles are associated with the European admixture characteristic of many current Native American populations ( Brown et al, 2017 ; Gravel et al, 2013 ; Keith et al, 2021 ; Klimentidis et al, 2009 ; Reich et al, 2012 ). Since the European hypopigmenting alleles may mask the effects of East Asian and Native American alleles, we searched for an admixed Native American population with high African, but low European admixture.…”