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
-
- 2,448
- views
-
- 316
- 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
-
- Computational and Systems Biology
- Genetics and Genomics
Untranslated regions (UTRs) contain crucial regulatory elements for RNA stability, translation and localization, so their integrity is indispensable for gene expression. Approximately 3.7% of genetic variants associated with diseases occur in UTRs, yet a comprehensive understanding of UTR variant functions remains limited due to inefficient experimental and computational assessment methods. To systematically evaluate the effects of UTR variants on RNA stability, we established a massively parallel reporter assay on 6555 UTR variants reported in human disease databases. We examined the RNA degradation patterns mediated by the UTR library in two cell lines, and then applied LASSO regression to model the influential regulators of RNA stability. We found that UA dinucleotides and UA-rich motifs are the most prominent destabilizing element. Gain of UA dinucleotide outlined mutant UTRs with reduced stability. Studies on endogenous transcripts indicate that high UA-dinucleotide ratios in UTRs promote RNA degradation. Conversely, elevated GC content and protein binding on UA dinucleotides protect high-UA RNA from degradation. Further analysis reveals polarized roles of UA-dinucleotide-binding proteins in RNA protection and degradation. Furthermore, the UA-dinucleotide ratio of both UTRs is a common characteristic of genes in innate immune response pathways, implying a coordinated stability regulation through UTRs at the transcriptomic level. We also demonstrate that stability-altering UTRs are associated with changes in biobank-based health indices, underscoring the importance of precise UTR regulation for wellness. Our study highlights the importance of RNA stability regulation through UTR primary sequences, paving the way for further exploration of their implications in gene networks and precision medicine.
-
- Genetics and Genomics
Flavin-containing monooxygenases (FMOs) are a conserved family of xenobiotic enzymes upregulated in multiple longevity interventions, including nematode and mouse models. Previous work supports that C. elegans fmo-2 promotes longevity, stress resistance, and healthspan by rewiring endogenous metabolism. However, there are five C. elegans FMOs and five mammalian FMOs, and it is not known whether promoting longevity and health benefits is a conserved role of this gene family. Here, we report that expression of C. elegans fmo-4 promotes lifespan extension and paraquat stress resistance downstream of both dietary restriction and inhibition of mTOR. We find that overexpression of fmo-4 in just the hypodermis is sufficient for these benefits, and that this expression significantly modifies the transcriptome. By analyzing changes in gene expression, we find that genes related to calcium signaling are significantly altered downstream of fmo-4 expression. Highlighting the importance of calcium homeostasis in this pathway, fmo-4 overexpressing animals are sensitive to thapsigargin, an ER stressor that inhibits calcium flux from the cytosol to the ER lumen. This calcium/fmo-4 interaction is solidified by data showing that modulating intracellular calcium with either small molecules or genetics can change expression of fmo-4 and/or interact with fmo-4 to affect lifespan and stress resistance. Further analysis supports a pathway where fmo-4 modulates calcium homeostasis downstream of activating transcription factor-6 (atf-6), whose knockdown induces and requires fmo-4 expression. Together, our data identify fmo-4 as a longevity-promoting gene whose actions interact with known longevity pathways and calcium homeostasis.
