Origins, admixture dynamics and homogenization of the African gene pool in the Americas

Abstract

53 4169-007, Portugal. 54 21 CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, Vairão, 4485-55 661, Portugal. 56 Abstract 76 The Transatlantic Slave Trade transported more than 9 million Africans to the Americas 77 between the early 16th and the mid-19th centuries. We performed genome-wide 78 analysis of 6,267 individuals from 22 populations and observed an enrichment in West-79 African ancestry in northern latitudes of the Americas, whereas South/East African 80 ancestry is more prevalent in southern South-America. This pattern results from distinct 81 geographic and geopolitical factors leading to population differentiation. However, we 82 observed a decrease of 68% in the African gene pool between-population diversity 83 within the Americas when compared to the regions of origin from Africa, underscoring 84 the importance of historical factors favoring admixture between individuals with 85 different African origins in the New World. This is consistent with the excess of West-86 Central Africa ancestry (the most prevalent in the Americas) in the US and Southeast-87 Brazil, respect to historical-demography expectations. Also, in most of the Americas, 88 admixture intensification occurred between 1,750 and 1,850, which correlates strongly 89 with the peak of arrivals from Africa. This study contributes with a population genetics 90 perspective to the ongoing social, cultural and political debate regarding ancestry, race, 91 and admixture in the Americas.92 93 Significance Statement 94 Differently from most genetic studies, that have estimated the overall African ancestry 95 in the Americas, we perform a finer geographic analysis and infer how different African 96 groups contributed to North-, South-American and Caribbean populations, in the 97 context of geographic and geopolitical factors. We also perform a formal comparison of 98 information from demographic history records of the Transatlantic Slave Trade with 99 inferences based on genomic diversity of current populations. Our approach reveals the 100 6 distinct regional African ancestry roots of different populations from North-, South-101 America and the Caribe and other important aspects of the historical process of 102 mestizaje and its dynamics in the American continent. 103 104 157(from Ghana, mean: 18%) ( Fig. 2A and B, SI Appendix, Table S3). 158The Western Africa-associated ancestry cluster has its highest proportions in Puerto 159 Ricans (38% of African ancestry), Colombians (27%) and US African-Americans (19-160 20%, purple in Fig. 1, SI Appendix, Table S1), while Brazilians have the lowest 161 proportion (<9%), limited to a Mandinka-like (Gambia) contribution and with no 162

Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21

“…GWAS of a Latino sample from a previous study, the POFC Multiethnic study (24), reported suggestive association at this genomic region (see Figure 1 in (23)). That Latino sample included diverse Hispanic groups from the US, Guatemala, Argentina, and Colombia, and all of the current WGS Colombia trios were part of the POFC Multiethnic study.…”

“…Given the population history of Colombians, causal OFC variants are may have arisen from one particular ancestral group, and such variants may be more frequent (and therefore more informative) among Colombians. The origin of African ancestry of Colombians is different from that of the other Latino populations (24). We therefore looked at the frequencies of the Colombian risk alleles across different populations.…”

Genetic admixture in Brazil

“…In an extensive study of the African Diaspora into the American continent, Gouveia et al (2020) used chromopainter , a program developed by Lawson, Hellenthal, Myers, and Falush (2012), and captured a continental trend: in most of the Americas, intercontinental admixture intensification occurred between 1750 and 1850, which correlates with the peak of arrivals of slaves from Africa, as suggested by a systematic comparison of the genomic data and the historical demography SlaveVoyage database (https://www.slavevoyages.org), which implies that this time interval was critical to shape the structure of the African gene pool in the New World.…”

Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21

“…To date, there have been 52 genome-wide associations reported and replicated between non-syndromic CL/P and genetic markers (NHGRI-EBI Catalog of published genome studies) (Buniello et al 2019), but as for most other complex human traits (Hazelett et al 2016;Tak and Farnham 2015;Zhu et al 2017), very few putative functional variants for non-syndromic OFCs have been identified from genome-wide association studies (GWASs) (Beaty et al 2016). In particular, the high heritability for OFC, estimated at 90% by a twin study in a Danish sample (Grosen et al 2011) cannot be explained by all identified common variants significantly associated with OFC, sometimes referred to as the "missing heritability" problem (Manolio et al 2009). Additional approaches will be necessary to expand our understanding of genetic variation in non-syndromic OFCs and whole genome sequencing (WGS) holds the promise of teasing out the so-called missing heritability from GWASs of OFC and other complex traits (Wainschtein et al 2019).…”