Genome-wide data from the Bubi of Bioko Island clarifies the Atlantic fringe of the Bantu dispersal

Abstract

Background Bioko is one of the few islands that exist around Africa, the most genetically diverse continent on the planet. The native Bantu-speaking inhabitants of Bioko, the Bubi, are believed to have colonized the island about 2000 years ago. Here, we sequenced the genome of thirteen Bubi individuals at high coverage and analysed their sequences in comparison to mainland populations from the Gulf of Guinea. Results We found that, genetically, the closest mainland population to the Bubi are Bantu-speaking groups from Angola instead the geographically closer groups from Cameroon. The Bubi possess a lower proportion of rainforest hunter-gatherer (RHG) ancestry than most other Bantu-speaking groups. However, their RHG component most likely came from the same source and could have reached them by gene flow from the mainland after island settlement. By studying identity by descent (IBD) genomic blocks and runs of homozygosity (ROHs), we found evidence for a significant level of genetic isolation among the Bubi, isolation that can be attributed to the island effect. Additionally, as this population is known to have one of the highest malaria incidence rates in the world we analysed their genome for malaria-resistant alleles. However, we were unable to detect any specific selective sweeps related to this disease. Conclusions By describing their dispersal to the Atlantic islands, the genomic characterization of the Bubi contributes to the understanding of the margins of the massive Bantu migration that shaped all Sub-Saharan African populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5529-0) contains supplementary material, which is available to authorized users.

Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans

“…Several ancient DNA (aDNA) studies have shown that the overall genetic structure was shaped by three ancestral and over-imposed genomic components respectively deriving from the Mesolithic hunter-gatherers, the Early Neolithic farmers, and the steppe nomads that entered Europe from the East around 5,000 years ago 3-7 . However, it is expected that the genetic homogenisation of the European populations during the last two millennia complicates our ability to discern subtle changes in ancestry by using some common population genetic tools.Complementary to these analyses, the distribution of so-called identity by descent (IBD) genomic stretches, which are co-inherited genetic segments delimited by recombination events, can provide information on more recently shared ancestry among individuals [8][9][10] . Such genomic block characterization in current populations has demonstrated the presence of co-ancestry across geographically distant Europeans shared over the last few thousand years, and revealed more recently shared co-ancestry in neighboring populations 11 .…”

“…Complementary to these analyses, the distribution of so-called identity by descent (IBD) genomic stretches, which are co-inherited genetic segments delimited by recombination events, can provide information on more recently shared ancestry among individuals [8][9][10] . Such genomic block characterization in current populations has demonstrated the presence of co-ancestry across geographically distant Europeans shared over the last few thousand years, and revealed more recently shared co-ancestry in neighboring populations 11 .…”

The Genes of Freedom: Genome-Wide Insights into Marronage, Admixture and Ethnogenesis in the Gulf of Guinea

“…During the first half of the 16th century, the archipelago of São Tomé and Príncipe, located in the Gulf of Guinea (1 • N, 7 • E), became one of the first examples of the so-called "plantation complex", which was soon to take over the New World [1] (Figure 1a). When the Portuguese reached the Gulf of Guinea in the early 1470s, they found the islands of São Tomé (860 km 2 ), Príncipe (136 km 2 ) and Annobón (17 km 2 ) to be uninhabited. A fourth island, Fernando Pó (now Bioko), located only 32 km off the coast of Cameroon, had already been populated by the Bubi, an autochthonous Bantu-speaking group who had presumably reached its shores by canoe [2].…”

“…When the Portuguese reached the Gulf of Guinea in the early 1470s, they found the islands of São Tomé (860 km 2 ), Príncipe (136 km 2 ) and Annobón (17 km 2 ) to be uninhabited. A fourth island, Fernando Pó (now Bioko), located only 32 km off the coast of Cameroon, had already been populated by the Bubi, an autochthonous Bantu-speaking group who had presumably reached its shores by canoe [2]. While São Tomé and Príncipe were both settled in the last decade of the 15th century, the permanent settlement of Annobón only started in the mid-16th century, and the island always remained sparsely populated until it was ceded to Spain, together with Bioko, in 1778.…”

“…The cultural interactions that characterized the peopling of São Tomé and Príncipe led to the emergence of three distinct Portuguese-related creole languages: (1) Santome (also Lungwa Santome) is spoken by about 60,000 of São Tomé's 180,000 inhabitants who identify themselves as Forros (literally "free slaves"), as they mostly descend from slaves that were granted manumission throughout the history of the island [7]; (2) Angolar (also Lunga Ngola) is spoken by approximately 10,000 individuals in the northwestern and southeastern parts of the island of São Tomé by the so-called Angolares, the descendants of a self-governed community whose exact origin remains unknown [4,7,8]; (3) Principense (also Lung'Ie) is a severely endangered language that is presently spoken by less than 100 of Príncipe's 7000 residents. Lung'Ie speakers, also known as Principenses, trace their roots to slaves brought to the island [9].…”