- Genome-wide data from the Bubi of Bioko Island clarifies the Atlantic fringe of the Bantu dispersal. - Background: Bioko is one of the few islands that exist around Africa, the most genetically diverse continent on the planet. - 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. - 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. - 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.. - The Gulf of Guinea, which covers a large portion of the African coast, is characterized by complex and rich eco- systems. - Of the few islands located in Atlantic Africa, four of them are found within the Gulf of Guinea (Fig. - The closest Bantu language on the mainland is most likely Galoa, which is spoken by Bantu-speaking groups of the Ogowe basin in Gabon [2]. - The Bubi have a distinct and unique culture among Bantu-speaking people [3], in- cluding the belief that different spiritual beings reside in specific geographical locations along the island and the existence of well-defined matrilineal clans [4].. - The origin of the Bubi people is controversial. - However, it is currently accepted that the Bubi agriculturalists arrived from the mainland in dugout canoes about 2000 years ago during the Late. - Full list of author information is available at the end of the article. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Ever since, the Bubi seem to have been isolated from mainland Bantu-speaking groups [9]. - The expansion of the Bantu-speaking farming commu- nities is probably one of the most important human movements that have taken place in recent African his- tory [10]. - By measuring the length of the introgressed genetic fragments, the. - 1 a Map of the Gulf of Guinea showing the location of Bioko Island and the neighbouring countries. - b Map of the Bioko Island. - There are hypothesis that could potentially be ex- plored with genome-wide data from the Bubi. - First, their relatively long period of isolation on the island is a potential way to test the age and extent of the Bantu ad- mixture with RHG tribes, an event that supposedly took place among the coastal Bantu groups after isolation of Bubi ancestors on the island. - Second, studying a tribe from one of the few islands around Africa could provide information about potential effects of endogamy and iso- lation that are less likely to occur in mainland tribes.. - Finally, genome-wide data from the Bubi can offer clues regarding the adaptation of this group to local condi- tions. - For example, it is known that the population of Equatorial Guinea has one of the highest levels of mal- aria infection in the world [25] and ranks 13th in the list of malaria prevalence countries, representing the second highest cause of death in the country [26] Despite pre- vention efforts carried out since 2004, severe malaria prevalence in Bioko children remains high [27]. - We show in this work that the Bantu population of Bioko Island mirrors the genetic makeup of the extant, coastal Bantu-speaking groups, also clarifying the dy- namics of this human expansion into the Atlantic islands of Africa.. - All mtDNA haplogroups present in the Bubi are subclades of the L haplogroup (L1b, L2b, L3e, L3f, and L3e) and are common in other populations from the Gulf of Guinea. - All male individuals of this dataset belong to subclades of the E1b1a1 haplogroup, the predominant Y-chromosome lineage in Western, Central and South- ern Africa (Additional file 1: Table S6).. - On a genome-wide scale, the first two components of the principal component analysis (PCA) separate the RHG from the Bantu speakers and the Western Africa. - X, chimpanzee), to examine the homogeneity of the Bubi population (Additional file 2: Figure S2, Additional file 1: Table S7).. - None of the tested populations showed elevated. - therefore we have treated the Bubi as a single population in subsequent analyses.. - 2 and Additional file 2: Figure S3) shows that the Bubi contain the same components as the other Bantu-speaking pop- ulations of the dataset but lower levels of the RHG com- ponent (in grey) than most of the mainland Bantu-speaking populations (with those from Angola be- ing the exception). - Some of the remaining ADMIXTURE plots (K = 2–15) (Additional file 2: Figure S4) also indi- cate potential substructuring among the Bubi. - Furthermore, owing to the colonial history of Bioko we have explored the possibility of some Iberian contri- bution to the Bubi ancestry by calculating the f 3 statistic in the form (Iberia, X. - The Bubi are placed within the range of Western African and other Bantu-speaking populations (Additional file 2: Figure S6). - Low levels of F st statistic indicate that the tested popula- tions share a large proportion of the genotypes, while high levels are indicators of genetic differentiation.. - The lowest values of genome-wide F st for the Bubi are again with Bantu-speaking Angolan groups (Kimbundu, F st = 0.0045. - On the other hand, we found that the Bubi dis- played the highest F st values when compared with RHG populations (Additional file 1: Table S9).. - Using this approach, the matrix and the resulting dendrogram confirm that the closest popula- tions to the Bubi are the Ovimbundu (Fig. - Interest- ingly, the Bubi are divided into two different clusters (Additional file 1: Table S7), one including only individ- uals from Bioko Island and the other shared with other Bantu-speaking groups. - To explore possible admixture events that could have led to the origins of the Bubi, we also performed GLOBETROTTER analysis (based on ChromoPainter);. - In this analysis, the Bubi present a clear intermediate position between Western African and Bantu-speaking populations (Additional file 2:. - We found the Bubi to share the highest number of IBD. - The structure of the matrix has been adapted using the fineSTRUCTURE dendrogram. - Add- itionally, we estimated the average of runs of homozy- gosity (ROHs) in each population, as well as the fraction of the genome in homozygosity as signals of endogamy.. - We found that all Bubi individuals possessed the malaria-resistant allele of the ACKR1 [30] and CD36 genes [31], in addition to certain variations in other genes such as G6PD [32], ATP2B4 [33], GRK5 [34], and IL-10 [35]. - However, considering these mutations are observed at low frequency among other African groups, it is likely they were simply not present in the ancestors of the Bubi (Additional file 1: Table S14). - We compared the allelic frequencies of malaria SNPs in the Bubi with those from neighbouring populations of the Gulf of Guinea – such as Esan, Gambian, Mende, and Yoruba – for which genome-wide sequence data was available. - Our genomic study of the population of Bioko Island confirms that the Bantu-speaking migration that shaped most of the present-day human diversity in Sub-Saharan Africa [40] also had a significant impact on African islands of the Gulf of Guinea. - The general components of ancestry found in the Bubi are not different from those found in mainland Bantu-speaking groups, al- though in the case of the Bubi, the RHG ancestry is lower than the amount detected in most Western Bantu-speaking groups. - Moreover, we did not detect a significant difference in the origin of the Bubi RHG gen- etic signal to the one observed in other Bantu popula- tions. - One potential explanation could be that an admixture event between the ancestors of the Bubi and the RHG tribes started about 2000 years ago and was brought to the island upon settlement, but continued to increase thereafter in most mainland Bantu-speaking groups. - This scenario could help explain the cluster- ing of the Bubi with Western African groups in some analyses (the latter groups also show residual or no traces of RHG ancestry).. - 6 a Average of the genome in homozygosity (in kb) for the Bubi and mainland Bantu populations. - b Average of the shared IBD genomic blocks between the Bubi and mainland Bantu populations (IBDs >. - interestingly, one of these individuals is from Bariobé, a relatively isolated province in the mountainous interior of the island. - An alternative possibility could be that the small fraction of RHG ancestry was acquired by gene flow from coastal regions after the ancestors of the Bubi settled in Bioko.. - In fact, although the slave trade was not so important in Bioko, it was very active in other coastal centres of the Gulf of Guinea, es- pecially in some of the minor islands such as Corisco and Annobón [42]. - Nonetheless, due to the cultural par- ticularities of the Bubi and the clear genetic signals of endogamy and isolation, it seems unlikely they would assimilate a significant number of foreign people. - In addition, no signals of potential Iberian admixture have been detected among the Bubi.. - Within the Bantu-speakers, the Bubi are more closely related to Angolan than to the geographically closer Cameroon groups (this is supported for instance by fineSTRUCTURE or f 3 statistics). - The Bubi seem to have experienced a certain history of isolation that left a mark in their genomes. - Out of all the Bantu-speaking groups, for instance, we found that the Bubi have some of the highest levels of IBD tracks shared among members of the same population, a signal of low diversity that is compatible with endogamy. - In fact, in the ROH analysis, the Bubi rank as the second most endogamous Bantu-speaking group, only after the Bekwil. - Nevertheless, the fact that the Bubi do not show a large genetic differentiation from potential source pop- ulations along the coast also indicates that drift did not have time to operate at large scale and that colonization of the island did not occur a long time ago.. - knowlesi, seems to be fixed, or at least is present at extremely high frequencies, in the Bubi population. - At the beginning of the twenty-first century, malaria was re- sponsible for a child mortality rate of 152 per every 1000 births in Bioko island, a figure that is only beginning to decrease thanks to recent malaria control projects [27].. - However, due to the limited sampling size and re- stricted distribution within Bioko, our study has to be considered as a preliminary assessment of the current Bubi genetic diversity. - In addition to the general population affinities of the Bubi, we have unveiled genetic evidences of a certain de- gree of isolation, which can be related to the insular con- ditions. - Our study of the genomic com- position of the Bubi not only adds further information to the current genetic diversity within Africa and its At- lantic islands, but also points to the importance of the genome-wide analyses in unravelling population affin- ities, selective pressures and past migrations that can be correlated with linguistic and archaeological information.. - We conclude that the origins of the Bantu expansion still needs further research and that future retrieval of ancient genomes from Central and Western Africa could shed need light on the cradle of the Bantu migrations.. - All thirteen individuals analysed in this study are mem- bers of the Cultural Bubi Association of Fuenlabrada, Madrid (Spain). - We discarded 25 of the interviewed individuals because of admixed ancestry. - Even though most of the individuals were not born in Bioko, we verified that the selected individuals had all grandparents born in the island. - many of the volunteers’ direct ancestors come. - We excluded any vari- ant with less than 70% of the main depth coverage or more than 200%. - Based on the colonial history of Bioko, we have assessed the presence of potential genetic admixture of the Bubi with Spanish individuals, adding Iberian samples from 1000 Genomes [52] to the SNP dataset. - For most of the analyses, we have extracted a sub-dataset with representative populations from West- ern and Central Africa. - Some of the population genomics analysis require an unrelated outgroup to the tested populations. - The resulting African dataset –including the Bubi- comprises 130,647 SNPs present in 1259 individuals.. - To situate the Bubi within the present diversity of the Gulf of Guinea and Western Africa, a principal compo- nents analysis (PCA) with the reduced dataset was gen- erated using EIGENSOFT software [58], Results were plotted using R package ggplot2 [59, 60].. - ADMIXTURE plots were generated to estimate the proportions of K ancestral components on each individ- ual genome [61] of the reduced dataset. - These combinations allow us to dissect the genetic admixture of the tested popula- tions with the Bubi in relation to all the representative source of genetic ancestry in Western Africa: Eastern RHG, Western RHG, Western-African populations and Bantu-speaking populations.. - the rest of the parameters were assigned by default. - We then filtered the IBD segments to keep only those that were shared by any Bubi and another individual of the dataset (including the IBD fragments shared by two Bubi individuals). - To reduce the impact that the population size could have on the global counts of IBD blocks per population, we corrected the value of the shared IBD fragments (IBDn) by the population size (t). - In order to obtain the average of the IBD blocks shared by any Bubi with any other in- dividual or population, we divided each number ob- tained in the previous step by the number of Bubi individuals, 13:ratioBubi_pop = (IBDn/t)/13.. - First, we calculated the average (in kilobases) of the gen- ome that it is in homozygosis for each population. - Sec- ond, we calculated the average of the number of genomic fragments that are in homozygosis for each population.. - Fisher’s exact test was used to determine the statistical signifi- cance of the observed differences (p <. - Evaluation of the effects of limited sample size. - We have used a whole genome F st approach to evaluate the effects of the small sample size used in this work.. - Sequenced reads of the 13 Bubi people analysed in the present study have been submitted to European Nucleotide Archive under the accession numbers: ERR2640217-ERR2640226.. - Phylogeography of the human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa. - At the southeast fringe of the bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes. - Cultural phylogeography of the bantu languages of sub-Saharan Africa. - The Slave Trade: The story of the Atlantic slave trade . - Comparative bantu: an introduction to the comparative linguistics and prehistory of the bantu languages. - Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. - Genetic evidence for two founding populations of the Americas.
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