Reconstructing the Population Genetic History of the Caribbean

Abstract

The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola), two mainland (Honduras, Colombia), and three Native South American (Yukpa, Bari, and Warao) populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA) method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse—which today is reflected by shorter, older ancestry tracts—consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse—reflected by longer, younger tracts—is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub-continental source populations with far greater resolution than previously thought, even when limited pre-Columbian Caribbean haplotypes have survived.

The Genetic Diversity of the Americas

“…These findings are consistent with historical information suggesting that approximately 68% and 32% of African slaves introduced to Brazil originated in westcentral/southeast and West Africa, respectively (84). Subsequent mtDNA and highdensity genotype analyses have confirmed and extended these results, highlighting areas of non-Bantu speakers in northwest and west-central Africa as major sources for the slaves brought to the Americas, with relatively smaller contributions from other regions, such as east African (Bantu-speaking) areas (18,48,57,63,98). Some regional variation has been reported for the relative importance of specific African source regions in the Americas; for instance, the non-Bantu component is more frequent in southern than northern Brazil, in agreement with historical information on the predominant origin of slaves introduced to different parts of this country (48).…”

Effect of Genetic African Ancestry on eGFR and Kidney Disease

“…In our study, the H/LA population exhibited an average of 29% (range=0%-100%) African ancestry, which reflects the predominantly (approximately 80%) Caribbean origin of the H/LA participants. 28 Higher levels of serum creatinine in individuals of African ancestry compared with other ethnic groups have been attributed to larger muscle mass and differences in tubular creatinine secretion. 2,27,29 Our findings strongly support that genetic ancestry is predictive of physiologic differences in both serum creatinine and eGFR.…”

Origin and dynamics of admixture in Brazilians and its effect on the pattern of deleterious mutations

“…African slaves arrived to Brazil during four centuries, whereas most arrivals to the United States occurred along two centuries, and the geographic and ethnic origin of Brazilian slaves differ from Caribbeans and African Americans (27). In fact, the Portuguese Crown imported slaves to Brazil from western and central west Africa (the two are the major sources of the slave trade to all of the Americas) as well as Mozambique.…”

“…Considering our SNPs density, we defined a window length of 100 SNPs following the work by Moreno-Estrada et al (27). PCAdmix infers the ancestry of each window.…”