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Korunes KL, Soares-Souza GB, Bobrek K, Tang H, Araújo II, Goldberg A, Beleza S. Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans. G3 GENES|GENOMES|GENETICS 2022; 12:6647844. [PMID: 35861404 PMCID: PMC9526050 DOI: 10.1093/g3journal/jkac183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022]
Abstract
Genetic data can provide insights into population history, but first, we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde’s well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde’s historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
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Affiliation(s)
| | | | - Katherine Bobrek
- Department of Anthropology, Emory University , Atlanta, GA 30322, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Isabel Inês Araújo
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde (Uni-CV) , Praia, Ilha de Santiago CP 379C, Cabo Verde
| | - Amy Goldberg
- Evolutionary Anthropology, Duke University , Durham, NC 27705, USA
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester , Leicester LE1 7RH, UK
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Hamid I, Korunes KL, Beleza S, Goldberg A. Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde. eLife 2021; 10:e63177. [PMID: 33393457 PMCID: PMC7815310 DOI: 10.7554/elife.63177] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Humans have undergone large migrations over the past hundreds to thousands of years, exposing ourselves to new environments and selective pressures. Yet, evidence of ongoing or recent selection in humans is difficult to detect. Many of these migrations also resulted in gene flow between previously separated populations. These recently admixed populations provide unique opportunities to study rapid evolution in humans. Developing methods based on distributions of local ancestry, we demonstrate that this sort of genetic exchange has facilitated detectable adaptation to a malaria parasite in the admixed population of Cabo Verde within the last ~20 generations. We estimate that the selection coefficient is approximately 0.08, one of the highest inferred in humans. Notably, we show that this strong selection at a single locus has likely affected patterns of ancestry genome-wide, potentially biasing demographic inference. Our study provides evidence of adaptation in a human population on historical timescales.
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Affiliation(s)
- Iman Hamid
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | | | - Sandra Beleza
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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Resende A, Amorim A, da Silva CV, Ribeiro T, Porto MJ, Costa Santos J, Afonso Costa H. Study of genetic markers of CODIS and ESS systems in a population of individuals from Cabo Verde living in Lisboa. Int J Legal Med 2017; 131:119-121. [DOI: 10.1007/s00414-016-1431-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
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Kaur M, Badaruddoza. Population genetic analysis of five northwest Punjabi endogamous groups using microsatellite markers. Meta Gene 2016. [DOI: 10.1016/j.mgene.2016.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Anagnostou P, Capocasa M, Dominici V, Montinaro F, Coia V, Destro-Bisol G. Evaluating mtDNA patterns of genetic isolation using a re-sampling procedure: A case study on Italian populations. Ann Hum Biol 2016; 44:140-148. [PMID: 27109644 DOI: 10.1080/03014460.2016.1181784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND A number of studies which have investigated isolation patterns in human populations rely on the analysis of intra- and inter-population genetic statistics of mtDNA polymorphisms. However, this approach makes it difficult to differentiate between the effects of long-term genetic isolation and the random fluctuations of statistics due to reduced sample size. AIM To overcome the confounding effect of sample size when detecting signatures of genetic isolation. SUBJECTS AND METHODS A re-sampling based procedure was employed to evaluate reduction in intra-population diversity, departure from surrounding genetic background and demographic stationarity in 34 Italian populations subject to isolation factors. RESULTS Signatures of genetic isolation were detected for all three statistics in seven populations: Pusteria valley, Sappada, Sauris, Timau settled in the eastern Italian Alps and Cappadocia, Filettino and Vallepietra settled in the Appenines. However, this study was unable to find signals for any of the statistics analysed in 19 populations. Finally, eight populations showing signals of isolation were found for one or two statistics. CONCLUSION The analysis revealed that the use of population genetic statistics combined with re-sampling procedure can help detect signatures of genetic isolation in human populations, even using a single, although highly informative, locus like mtDNA.
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Affiliation(s)
- Paolo Anagnostou
- a Dipartimento di Biologia Ambientale , Sapienza University of Rome , Rome , Italy.,b Istituto Italiano di Antropologia , Rome , Italy
| | - Marco Capocasa
- b Istituto Italiano di Antropologia , Rome , Italy.,c Dipartimento di Biologia e Biotecnologie 'Charles Darwin' , Sapienza University of Rome , Rome , Italy
| | - Valentina Dominici
- a Dipartimento di Biologia Ambientale , Sapienza University of Rome , Rome , Italy
| | | | - Valentina Coia
- e Istituto per le Mummie e l'Iceman, Accademia Europea di Bolzano (EURAC-Research) , Bolzano , Italy
| | - Giovanni Destro-Bisol
- a Dipartimento di Biologia Ambientale , Sapienza University of Rome , Rome , Italy.,b Istituto Italiano di Antropologia , Rome , Italy
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Beleza S, Campos J, Lopes J, Araújo II, Hoppfer Almada A, Correia e Silva A, Parra EJ, Rocha J. The admixture structure and genetic variation of the archipelago of Cape Verde and its implications for admixture mapping studies. PLoS One 2012; 7:e51103. [PMID: 23226471 PMCID: PMC3511383 DOI: 10.1371/journal.pone.0051103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/30/2012] [Indexed: 11/18/2022] Open
Abstract
Recently admixed populations offer unique opportunities for studying human history and for elucidating the genetic basis of complex traits that differ in prevalence between human populations. Historical records, classical protein markers, and preliminary genetic data indicate that the Cape Verde islands in West Africa are highly admixed and primarily descended from European males and African females. However, little is known about the variation in admixture levels, admixture dynamics and genetic diversity across the islands, or about the potential of Cape Verde for admixture mapping studies. We have performed a detailed analysis of phenotypic and genetic variation in Cape Verde based on objective skin color measurements, socio-economic status (SES) evaluations and data for 50 autosomal, 34 X-chromosome, and 21 non-recombinant Y-chromosome (NRY) markers in 845 individuals from six islands of the archipelago. We find extensive genetic admixture between European and African ancestral populations (mean West African ancestry = 0.57, sd = 0.08), with individual African ancestry proportions varying considerably among the islands. African ancestry proportions calculated with X and Y-chromosome markers confirm that the pattern of admixture has been sex-biased. The high-resolution NRY-STRs reveal additional patterns of variation among the islands that are most consistent with differentiation after admixture. The differences in the autosomal admixture proportions are clearly evident in the skin color distribution across the islands (Pearson r = 0.54, P-value<2e–16). Despite this strong correlation, there are significant interactions between SES and skin color that are independent of the relationship between skin color and genetic ancestry. The observed distributions of admixture, genetic variation and skin color and the relationship of skin color with SES relate to historical and social events taking place during the settlement history of Cape Verde, and have implications for the design of association studies using this population.
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Affiliation(s)
- Sandra Beleza
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
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Spínola C, Brehm A, Spínola H. Alpha-1-antitrypsin deficiency in the Cape Verde islands (Northwest Africa): High prevalence in a sub-Saharan population. Respir Med 2010; 104:1069-72. [PMID: 20226649 DOI: 10.1016/j.rmed.2010.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/11/2010] [Accepted: 02/15/2010] [Indexed: 10/19/2022]
Abstract
Alpha-1-antitrypsin (AAT) deficiency results from mutations on the Protease Inhibitor (PI) locus located in chromosome 14 and has been associated with pulmonary early-onset emphysema and chronic obstructive pulmonary disease (COPD). African populations show a lower prevalence of AAT deficiency compared to Europeans. Two hundred and two (202) unrelated samples from the Cape Verde archipelago (Northwest Africa) were genotyped for the two most common AAT deficiency alleles, PI*S and PI*Z, using PCR - Mediated Site-Directed Mutagenesis. PI*S mutation in Cape Verde (3.2%) presents one of the highest frequencies in sub-Saharans, similar to South Africa (3.3%) but lower than Angolans (18.8%), Namibians (14.7%), Nigerians (6.4%) and Botswains (4.5%). The PI*Z mutation shows lower values (0.2%) than other sub-Saharan populations, namely Somalia (1.15%), Mali (0.98%)or Nigeria (0.36%). However, many other sub-Saharan populations, like Botswana, Congo, Cameroon, Angola, Gambia, South Africa, Mozambique and Namibia, lack the PI*Z mutation. The frequency of all the AAT deficiency genotypes in the Cape Verde archipelago (PI*ZZ, PI*SS, and PI*SZ) was estimated to be one of the highest in sub-Saharans (15 per 1000), only lower than Angola (54 per 1000) and Namibia (22 per 1000). The results obtained show a high prevalence of the AAT deficiency in Cape Verdeans when compared to other sub-Saharans a condition that can be explained by a heavy European genetic influence, characteristic of that population.
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Affiliation(s)
- Carla Spínola
- Human Genetics Laboratory, University of Madeira, Campus da Penteada, 9000-390 Funchal, Portugal.
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Alves J, Machado P, Silva J, Gonçalves N, Ribeiro L, Faustino P, do Rosário VE, Manco L, Gusmão L, Amorim A, Arez AP. Analysis of malaria associated genetic traits in Cabo Verde, a melting pot of European and sub Saharan settlers. Blood Cells Mol Dis 2009; 44:62-8. [PMID: 19837619 DOI: 10.1016/j.bcmd.2009.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 09/17/2009] [Indexed: 11/16/2022]
Abstract
Malaria has occurred in the Cabo Verde archipelago with epidemic characteristics since its colonization. Nowadays, it occurs in Santiago Island alone and though prophylaxis is not recommended by the World Health Organization, studies have highlight the prospect of malaria becoming a serious public health problem as a result of the presence of antimalarial drug resistance associated with mutations in the parasite populations and underscore the need for tighter surveillance. Despite the presumptive weak immune status of the population, severe symptoms of malaria are not observed and many people present a subclinical course of the disease. No data on the prevalence of sickle-cell trait and red cell glucose-6-phosphate dehydrogenase deficiency (two classical genetic factors associated with resistance to severe malaria) were available for the Cabo Verde archipelago and, therefore, we studied the low morbidity from malaria in relation to the particular genetic characteristics of the human host population. We also included the analysis of the pyruvate kinase deficiency associated gene, reported as putatively associated with resistance to the disease. Allelic frequencies of the polymorphisms examined are closer to European than to African populations and no malaria selection signatures were found. No association was found between the analyzed human factors and infection but one result is of high interest: a linkage disequilibrium test revealed an association of distant loci in the PKLR gene and adjacent regions, only in non-infected individuals. This could mean a more conserved gene region selected in association to protection against the infection and/or the disease.
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Affiliation(s)
- Joana Alves
- Centre for Malaria and Tropical Diseases, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
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Branco CC, Bento MS, Gomes CT, Cabral R, Pacheco PR, Mota-Vieira L. Azores Islands: Genetic origin, gene flow and diversity pattern. Ann Hum Biol 2009; 35:65-74. [DOI: 10.1080/03014460701793782] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gonçalves R, Freitas A, Branco M, Rosa A, Fernandes AT, Zhivotovsky LA, Underhill PA, Kivisild T, Brehm A. Y-chromosome lineages from Portugal, Madeira and Açores record elements of Sephardim and Berber ancestry. Ann Hum Genet 2006; 69:443-54. [PMID: 15996172 DOI: 10.1111/j.1529-8817.2005.00161.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A total of 553 Y-chromosomes were analyzed from mainland Portugal and the North Atlantic Archipelagos of Açores and Madeira, in order to characterize the genetic composition of their male gene pool. A large majority (78-83% of each population) of the male lineages could be classified as belonging to three basic Y chromosomal haplogroups, R1b, J, and E3b. While R1b, accounting for more than half of the lineages in any of the Portuguese sub-populations, is a characteristic marker of many different West European populations, haplogroups J and E3b consist of lineages that are typical of the circum-Mediterranean region or even East Africa. The highly diverse haplogroup E3b in Portuguese likely combines sub-clades of distinct origins. The present composition of the Y chromosomes in Portugal in this haplogroup likely reflects a pre-Arab component shared with North African populations or testifies, at least in part, to the influence of Sephardic Jews. In contrast to the marginally low sub-Saharan African Y chromosome component in Portuguese, such lineages have been detected at a moderately high frequency in our previous survey of mtDNA from the same samples, indicating the presence of sex-related gene flow, most likely mediated by the Atlantic slave trade.
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Affiliation(s)
- Rita Gonçalves
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, 9000-390 Funchal, Portugal
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Spínola H, Bruges-Armas J, Middleton D, Brehm A. HLA polymorphisms in Cabo Verde and Guiné-Bissau inferred from sequence-based typing. Hum Immunol 2005; 66:1082-92. [PMID: 16386651 DOI: 10.1016/j.humimm.2005.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Accepted: 08/31/2005] [Indexed: 11/30/2022]
Abstract
Human leukocyte antigen (HLA)-A, -B, and -DRB1 polymorphisms were examined in the Cabo Verde and Guiné-Bissau populations. The data were obtained at high-resolution level, using sequence-based typing. The most frequent alleles in each locus was: A*020101 (16.7% in Guiné-Bissau and 13.5% in Cabo Verde), B*350101 (14.4% in Guiné-Bissau and 13.2% in Cabo Verde), DRB1*1304 (19.6% in Guiné-Bissau), and DRB1*1101 (10.1% in Cabo Verde). The predominant three loci haplotype in Guiné-Bissau was A*2301-B*1503-DRB1*1101 (4.6%) and in Cabo Verde was A*3002-B*350101-DRB1*1001 (2.8%), exclusive to northwestern islands (5.6%) and absent in Guiné-Bissau. The present study corroborates historic sources and other genetic studies that say Cabo Verde were populated not only by Africans but also by Europeans. Haplotypes and dendrogram analysis shows a Caucasian genetic influence in today's gene pool of Cabo Verdeans. Haplotypes and allele frequencies present a differential distribution between southeastern and northwestern Cabo Verde islands, which could be the result of different genetic influences, founder effect, or bottlenecks. Dendrograms and principal coordinates analysis show that Guineans are more similar to North Africans than other HLA-studied sub-Saharans, probably from ancient and recent genetic contacts with other peoples, namely East Africans.
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Affiliation(s)
- Hélder Spínola
- Human Genetics Laboratory, University of Madeira, Campus of Penteada, Funchal, Portugal
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Cabo Verde islands: different maternal and paternal heritage testifies the nature of its first settlers. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0531-5131(03)01770-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Brehm A, Pereira L, Kivisild T, Amorim A. Mitochondrial portraits of the Madeira and Açores archipelagos witness different genetic pools of its settlers. Hum Genet 2003; 114:77-86. [PMID: 14513360 DOI: 10.1007/s00439-003-1024-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2003] [Accepted: 08/08/2003] [Indexed: 11/30/2022]
Abstract
We have studied the matrilineal genetic composition of the Madeira and Açores north Atlantic archipelagos, which were settled by the Portuguese in the 15th century. Both archipelagos, and particularly Madeira, were involved in a complex commercial network established by the Portuguese, which included the trading of slaves across the Atlantic. One hundred and fifty-five mtDNAs sampled from the Madeira and 179 from the Açores archipelagos were analysed for the hypervariable segment I (HVS-I), and for haplogroup-diagnostic coding-region RFLPs. The different settlement histories of both groups of islands are well reflected in their present day mtDNA pool. Although both archipelagos show identical diversity values, they are clearly different in their haplogroup content. Madeira displays a stronger sub-Saharan imprint, with haplogroups L1-L3 constituting about 13% of the lineages. Also, the relative frequencies of L sub-clusters in Madeira and mainland Portugal suggests that, at least in part, African presence in Madeira can be attributed to a direct gene flow from West Africa and not via Portugal. A comparison of the genetic composition of these two archipelagos with the Canary Islands, specially taking into account that their European source population was essentially from the Iberian Peninsula, testifies the stronger impact of the North African U6 cluster in the Canaries. This group is present in Madeira at a moderate frequency, but very reduced in the Açores. Nevertheless the recorded introduction of Canary native Guanches, who are characterized by the presence of particular sub-clade U6b1, has left no detectable imprints in the present day population of Madeira.
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Affiliation(s)
- António Brehm
- Human Genetics Laboratory, Centre of Macaronesian Studies, University of Madeira, Campus of Penteada, 9000 Funchal, Portugal.
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