A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde
- CNRS-MNHN-Université Paris Cité, France
- Pennsylvania State University, United States
- CNRS-Université Paris-Dauphine- PSL University, France
- Uppsala University, Sweden
- Institut Pasteur, France
- Stanford University, United States
- University of Michigan-Ann Arbor, United States
Abstract
From the 15th to the 19th century, the Trans-Atlantic Slave-Trade (TAST) influenced the genetic and cultural diversity of numerous populations. We explore genomic and linguistic data from the nine islands of Cabo Verde, the earliest European colony of the era in Africa, a major Slave-Trade platform between the 16th and 19th centuries, and a previously uninhabited location ideal for investigating early admixture events between Europeans and Africans. Using local-ancestry inference approaches, we find that genetic admixture in Cabo Verde occurred primarily between Iberian and certain Senegambian populations, although forced and voluntary migrations to the archipelago involved numerous other populations. Inter-individual genetic and linguistic variation recapitulates the geographic distribution of individuals' birth-places across Cabo Verdean islands, following an isolation-by-distance model with reduced genetic and linguistic effective dispersals within the archipelago, and suggesting that Kriolu language variants have developed together with genetic divergences at very reduced geographical scales. Furthermore, based on approximate bayesian computation inferences of highly complex admixture histories, we find that admixture occurred early on each island, long before the 18th-century massive TAST deportations triggered by the expansion of the plantation economy in Africa and the Americas, and after this era mostly during the abolition of the TAST and of slavery in European colonial empires. Our results illustrate how shifting socio-cultural relationships between enslaved and non-enslaved communities during and after the TAST, shaped enslaved-African descendants’ genomic diversity and structure on both sides of the Atlantic.
Data availability
The novel genome-wide genotype data, the linguistic utterance counts, and the self-reported anthropo-logical data presented here can be accessed and downloaded via the European Genome-Phenome Ar-chive (EGA) database accession numbers EGAD00001008976, EGAD00001008977, EGAD00001008978, and EGAD00001008979. All datasets can be shared provided that future envi-sioned studies comply with the informed consents provided by the participants, and in agreement with institutional ethics committee's recommendations applying to this data.All data will be made publically available on eGA in the event of acceptance.
-
The admixture histories of Cabo VerdeEuropean Genome-Phenome Ar-chive (EGA) database accession numbers EGAD00001008976, EGAD00001008977, EGAD00001008978, EGAD00001008979.
-
1000 Genomes Project Phase 3International Genome Sample Resource (IGSR).
-
African Genome Variation ProjecteGA, EGAD00001000959.
Article and author information
Author details
Zachary Alfano Szpiech
Cesar A Fortes-Lima
Funding
Agence Nationale de la Recherche (ANR METHIS 15-CE32-0009-1)
- Romain Laurent
- Sergio S da Costa
- Valentin Thouzeau
- Cesar A Fortes-Lima
- Françoise Dessarps-Freichey
- José Utgé
- Paul Verdu
France-Stanford Center for Interdisciplinary Studies
- Noah A Rosenberg
National Institutes of Health (R35 GM146926)
- Zachary Alfano Szpiech
Marcus Borgströms Foundation for Genetic Research
- Cesar A Fortes-Lima
Bertil Lundman Foundation for Anthropological Studies
- Cesar A Fortes-Lima
University of Michigan Linguistics Department Faculty Research Funds
- Marlyse Baptista
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: Research sampling protocols followed the Declaration of Helsinki guidelines and the French laws of scientific research deontology (Loi n{degree sign} 2016-483 du 20 avril 2016). Research and ethics authorizations were provided by the Ministério da Saúde de Cabo Verde (228/DGS/11), Stanford University IRB (Protocol ID n{degree sign}23194-IRB n{degree sign}349), University of Michigan IRB (n{degree sign}HUM00079335), and the French ethics committees and CNIL (Declaration n{degree sign}1972648). All volunteer participants provided written and video-recorded informed consent.
Copyright
© 2023, Laurent et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,377
- views
-
- 304
- downloads
-
- 3
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
A genetic and linguistic analysis of the admixture histories of the islands of Cabo Verde
eLife 12:e79827.
https://doi.org/10.7554/eLife.79827
Further reading
-
- Genetics and Genomics
Heritable fragile bone disorders (FBDs), ranging from multifactorial to rare monogenic conditions, are characterized by an elevated fracture risk. Validating causative genes and understanding their mechanisms remain challenging. We assessed a semi-high throughput zebrafish screening platform for rapid in vivo functional testing of candidate FBD genes. Six genes linked to severe recessive osteogenesis imperfecta (OI) and four associated with bone mineral density (BMD) from genome-wide association studies were analyzed using CRISPR/Cas9-based crispant screening in F0 mosaic founder zebrafish. Next-generation sequencing confirmed high indel efficiency (mean 88%), mimicking stable knock-out models. Skeletal phenotyping at 7, 14, and 90 days post-fertilization (dpf) using microscopy, Alizarin Red S staining, and microCT was performed. Larval crispants showed variable osteoblast and mineralization phenotypes, while adult crispants displayed consistent skeletal defects, including malformed neural and haemal arches, vertebral fractures and fusions, and altered bone volume and density. In addition, aldh7a1 and mbtps2 crispants experienced increased mortality due to severe skeletal deformities. RT-qPCR revealed differential expression of osteogenic markers bglap and col1a1a, highlighting their biomarker potential. Our results establish zebrafish crispant screening as a robust tool for FBD gene validation, combining skeletal and molecular analyses across developmental stages to uncover novel insights into gene functions in bone biology.
-
- Genetics and Genomics
The prevalence of childhood obesity is increasing worldwide, along with the associated common comorbidities of type 2 diabetes and cardiovascular disease in later life. Motivated by evidence for a strong genetic component, our prior genome-wide association study (GWAS) efforts for childhood obesity revealed 19 independent signals for the trait; however, the mechanism of action of these loci remains to be elucidated. To molecularly characterize these childhood obesity loci, we sought to determine the underlying causal variants and the corresponding effector genes within diverse cellular contexts. Integrating childhood obesity GWAS summary statistics with our existing 3D genomic datasets for 57 human cell types, consisting of high-resolution promoter-focused Capture-C/Hi-C, ATAC-seq, and RNA-seq, we applied stratified LD score regression and calculated the proportion of genome-wide SNP heritability attributable to cell type-specific features, revealing pancreatic alpha cell enrichment as the most statistically significant. Subsequent chromatin contact-based fine-mapping was carried out for genome-wide significant childhood obesity loci and their linkage disequilibrium proxies to implicate effector genes, yielded the most abundant number of candidate variants and target genes at the BDNF, ADCY3, TMEM18, and FTO loci in skeletal muscle myotubes and the pancreatic beta-cell line, EndoC-BH1. One novel implicated effector gene, ALKAL2 – an inflammation-responsive gene in nerve nociceptors – was observed at the key TMEM18 locus across multiple immune cell types. Interestingly, this observation was also supported through colocalization analysis using expression quantitative trait loci (eQTL) derived from the Genotype-Tissue Expression (GTEx) dataset, supporting an inflammatory and neurologic component to the pathogenesis of childhood obesity. Our comprehensive appraisal of 3D genomic datasets generated in a myriad of different cell types provides genomic insights into pediatric obesity pathogenesis.
