Dataset Information

Struct-f4: a Rcpp package for ancestry profile and population structure inference from F4 statistics.

ABSTRACT: Visualisation and inference of population structure is increasingly important for fundamental and applied research. Here, we present Struct-f4, providing automated solutions to characterize and summarize the genetic ancestry profile of individuals, assess their genetic affinities, identify admixture sources and quantify admixture levels. Struct-f4 is written in Rcpp and relies on f4-statistics and MCMC optimization. It is freely available under GNU General Public License in Bitbucket (https://bitbucket.org/plibradosanz/structf4/). Supplementary data are available at Bioinformatics online.

SUBMITTER: Librado P

PROVIDER: S-EPMC8963280 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics.

Librado Pablo P Orlando Ludovic L

Bioinformatics (Oxford, England) 20220301 7

<h4>Summary</h4>Visualization and inference of population structure is increasingly important for fundamental and applied research. Here, we present Struct-f4, providing automated solutions to characterize and summarize the genetic ancestry profile of individuals, assess their genetic affinities, identify admixture sources and quantify admixture levels.<h4>Availability and implementation</h4>Struct-f4 is written in Rcpp and relies on f4-statistics and Markov Chain Monte Carlo (MCMC) optimization ...[more]

PMID: 35080599

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Project description: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.

Dataset Information

Struct-f4: a Rcpp package for ancestry profile and population structure inference from F4 statistics.

Publications

Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics.

Similar Datasets

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