The Genomic Legacy of the Transatlantic Slave Trade in the Yungas Valley of Bolivia

Abstract

During the period of the Transatlantic Slave Trade (TAST) some enslaved Africans were forced to move to Upper Peru (nowadays Bolivia). At first they were sent to Potosí, but later to the tropical Yungas valley where the Spanish colonizers established a so-called “hacienda system” that was based on slave labor, including African-descendants. Due to their isolation, very little attention has been paid so far to ‘Afro-Bolivian’ communities either within the research field of TAST or in genetic population studies. In this study, a total of 105 individuals from the Yungas were sequenced for their mitochondrial DNA (mtDNA) control region, and mitogenomes were obtained for a selected subset of these samples. We also genotyped 46 Ancestry Informative Markers (AIM) in order to investigate continental ancestry at the autosomal level. In addition, Y-chromosome STR and SNP data for a subset of the same individuals was also available from the literature. The data indicate that the partitioning of mtDNA ancestry in the Yungas differs significantly from that in the rest of the country: 81% Native American, 18% African, and 1% European. Interestingly, the great majority of ‘Afro-descendant’ mtDNA haplotypes in the Yungas (84%) concentrates in the locality of Tocaña. This high proportion of African ancestry in the Tocaña is also manifested in the Y-chromosome (44%) and in the autosomes (56%). In sharp contrast with previous studies on the TAST, the ancestry of about 1/3 of the ‘Afro-Bolivian’ mtDNA haplotypes can be traced back to East and South East Africa, which may be at least partially explained by the Arab slave trade connected to the TAST.

Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands

“…Other haplogroups present in the indigenous people are also observed in the modern population, including J2a2d, U6b1a and X3a. In line with previous analyses [27,31], a sub-Saharan African (L3d1b3a) [74] and an Amerindian lineage (A2) [75] are observed in the current population of the Canary Islands. Assuming that our set of 48 ancient genomes is representative of the native population, we performed a rough admixture estimate of 27.8% of maternal lineages in members of the present-day population possessing indigenous origins, while 61.1% would be of European ascription (Figure S3).…”

The peopling of South America and the trans-Andean gene flow of the first settlers

“…The map shows the great fit between archaeological and mtDNA evidence, then suggesting that B2 is a good marker of the demographic transformation occurring in the Andes. The highest frequencies of B2 in South America are by far in the Andean regions of Peru, Bolivia, and northern Argentina, reaching frequencies up to 70%-90% in some Aymara and Quechua Andean populations (Bert et al 2001;Barbieri et al 2011;Heinz et al 2013Heinz et al , 2015. The pre-Columbian mtDNA data available follow the same pattern: B2 reaches high frequencies in the Peruvian highlands, ranging from 42% to 75% (Shinoda et al 2006;Baca et al 2012Baca et al , 2014.…”

Mapping the genomic mosaic of two ‘Afro-Bolivians’ from the isolated Yungas valleys

“…Stimulated by the recent findings of Heinz et al [ 33 ] indicating the presence of mtDNA East African ancestry in the Yungas region, we tested for this ancestry in the autosomal genome of the two ‘Afro-Bolivians’ analyzed in the present study. In this regard, exploratory ADMIXTURE analysis suggested that the Luhya could, at least in part, explain the East African component observed in the Tocaña.…”

“…A collection of 105 saliva samples recruited from the Yunga’s region of Bolivia was previously characterized for mtDNA and a panel of Ancestry Informative Markers or AIMs [ 33 ]. A small subset of these samples was additionally analyzed for a selection of Y-chromosome markers [ 29 ].…”

“…In contrast, African ancestry was observed to be marginal in both mtDNA and autosomal DNA, respectively [ 23 , 24 , 32 ]. Only the community of Tocaña (Nor Yungas) still preserves the African genetic legacy of the TAST [ 33 ] as inferred from the uniparental markers and a few ancestry informative (autosomal) markers (AIMs).…”