Post by djoser-xyyman on Mar 13, 2019 8:36:39 GMT -5
Genome-wide data from the Bubi of Bioko Island clarifies the Atlantic fringe of the Bantu dispersal -
Pere Gelabert 2019
bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5529-0
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.
geographical locations along the island and the existence of well-defined matrilineal clans
The origin of the Bubi people is controversial. Since the British explorer Richard Francis Burton visited the island (then called Fernando Poo) in 1874 [5], ethnographers generally considered the Bubi to be the original settlers of Bioko. However, it is currently accepted that the Bubi agriculturalists arrived from the mainland in dugout canoes about 2000 years ago during the Late Neolithic
Bubi mythology explains that, upon their arrival to the island, they found other, more robust people living there, a population whom they called Balettérimo [1, 9].
In fact, some unsystematic archaeological prospects carried out by Spanish scholars have uncovered pre-Neolithic lithic tools of a typology that has been called banapense, although this lithic typology does not currently have a clear chronological framework [9].
So far, however, no ancient genomes have been retrieved from the Gulf of Guinea.
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 Southern Africa (Additional file 1: Table S6).
Three Bubi individuals that we named Bubi-subset1 (BBS014, BBS018, BBS023) fall within the Western Africa cluster showing that some individuals share a larger proportion of Western-Africa ancestry than others, while the rest (named Bubi-subset2) cluster within the Bantu diversity (Additional file 2: Figure S1).
? huh?!
To determine which mainland populations share a higher level of genetic ancestry with the Bubi, we tested all neighbouring populations with the outgroup f3 statistic (considering San as outgroup). Our results indicate that non-Bantu Western African populations such as Yoruba, Bariba, Fon and Azhizi, as well as Bantu-speaking groups from Angola such as Kongo, Ovimbundu and Kimbundu show more genetic affinities with the Bubi, apparently because they all show lower hunter-gatherer ancestry as compared to other groups
Bubi people seem to have very low levels of genetic admixture from the RHG populations; however, this small signal is absent in Western Africans.
possibility of some Iberian contribution to the Bubi ancestry by calculating the f3 therefore, no Iberian genetic affinities can be discerned within the current dataset.
this method clusters the populations into the same groups as those used when considering genotypes. In this analysis, the Bubi present a clear intermediate position between Western African and Bantu-speaking populations (Additional file 2: Figure S9). For computational convenience, we performed these analyses with a ***restricted dataset***.
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. We found statistically significant (Fisher’s exact test) differences in some alleles, but nothing that indicated a unique trend in the Bubi
Samples
All thirteen individuals analysed in this study are members of the Cultural Bubi Association of Fuenlabrada, Madrid (Spain). We obtained informed consent from all subjects. We discarded 25 of the interviewed individuals because of admixed ancestry; many of them had a recent Fang ancestor from the mainland. 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 from Malabo, Bariobé and Baney, which are located in the Northeast region of Bioko (Additional file 1: Table S1).
Covaris system and sequenced in HiSeqX10 (Illumina) with hiseq2x150bp settings plus 65 bp paired-end adapters at Macrogen (South Korea).
and the reads were mapped against the Human reference genome [National Center for Biotechnology Information (NCBI) 37, hg19] using Burrows-Wheeler Aligner (BWA) with default parameters
To ensure that genotypes were properly called after merging the dataset, the Yoruba SNP genotypes were compared against the 1000 Genomes Yoruba population. However, subsequent analyses were performed only with the Yoruba genotypes from Western Africa dataset
The resulting African dataset –including the Bubi- comprises 130,647 SNPs present in 1259 individuals.
After excluding all positions with at least one missing site, we ended up with a dataset of 491,203 variable positions with no missing data.
Availability of data and materials
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.
Pere Gelabert 2019
bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5529-0
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.
geographical locations along the island and the existence of well-defined matrilineal clans
The origin of the Bubi people is controversial. Since the British explorer Richard Francis Burton visited the island (then called Fernando Poo) in 1874 [5], ethnographers generally considered the Bubi to be the original settlers of Bioko. However, it is currently accepted that the Bubi agriculturalists arrived from the mainland in dugout canoes about 2000 years ago during the Late Neolithic
Bubi mythology explains that, upon their arrival to the island, they found other, more robust people living there, a population whom they called Balettérimo [1, 9].
In fact, some unsystematic archaeological prospects carried out by Spanish scholars have uncovered pre-Neolithic lithic tools of a typology that has been called banapense, although this lithic typology does not currently have a clear chronological framework [9].
So far, however, no ancient genomes have been retrieved from the Gulf of Guinea.
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 Southern Africa (Additional file 1: Table S6).
Three Bubi individuals that we named Bubi-subset1 (BBS014, BBS018, BBS023) fall within the Western Africa cluster showing that some individuals share a larger proportion of Western-Africa ancestry than others, while the rest (named Bubi-subset2) cluster within the Bantu diversity (Additional file 2: Figure S1).
? huh?!To determine which mainland populations share a higher level of genetic ancestry with the Bubi, we tested all neighbouring populations with the outgroup f3 statistic (considering San as outgroup). Our results indicate that non-Bantu Western African populations such as Yoruba, Bariba, Fon and Azhizi, as well as Bantu-speaking groups from Angola such as Kongo, Ovimbundu and Kimbundu show more genetic affinities with the Bubi, apparently because they all show lower hunter-gatherer ancestry as compared to other groups
Bubi people seem to have very low levels of genetic admixture from the RHG populations; however, this small signal is absent in Western Africans.
possibility of some Iberian contribution to the Bubi ancestry by calculating the f3 therefore, no Iberian genetic affinities can be discerned within the current dataset.
this method clusters the populations into the same groups as those used when considering genotypes. In this analysis, the Bubi present a clear intermediate position between Western African and Bantu-speaking populations (Additional file 2: Figure S9). For computational convenience, we performed these analyses with a ***restricted dataset***.
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. We found statistically significant (Fisher’s exact test) differences in some alleles, but nothing that indicated a unique trend in the Bubi
Samples
All thirteen individuals analysed in this study are members of the Cultural Bubi Association of Fuenlabrada, Madrid (Spain). We obtained informed consent from all subjects. We discarded 25 of the interviewed individuals because of admixed ancestry; many of them had a recent Fang ancestor from the mainland. 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 from Malabo, Bariobé and Baney, which are located in the Northeast region of Bioko (Additional file 1: Table S1).
Covaris system and sequenced in HiSeqX10 (Illumina) with hiseq2x150bp settings plus 65 bp paired-end adapters at Macrogen (South Korea).
and the reads were mapped against the Human reference genome [National Center for Biotechnology Information (NCBI) 37, hg19] using Burrows-Wheeler Aligner (BWA) with default parameters
To ensure that genotypes were properly called after merging the dataset, the Yoruba SNP genotypes were compared against the 1000 Genomes Yoruba population. However, subsequent analyses were performed only with the Yoruba genotypes from Western Africa dataset
The resulting African dataset –including the Bubi- comprises 130,647 SNPs present in 1259 individuals.
After excluding all positions with at least one missing site, we ended up with a dataset of 491,203 variable positions with no missing data.
Availability of data and materials
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.
