Basal West African Explained

Basal West African is a hypothetical line of descent[1] [2] that is no longer extant.[3]

History

Utilizing Western Africans (e.g., Esan of Nigeria, Mende of Sierra Leone, western Gambians), the divergence of a set of early modern or archaic humans, numbering around 25,000 or between 23,000 and 27,000, from either the last common ancestor of the San people and all other modern humans, or humans and Neanderthals, is approximated to have occurred between 1,020,000 BP and 360,000 BP.[4] Between 124,000 BP and 0 BP, 2% – 19% of the genes may have introgressed into ancestors of modern West Africans as a result of admixture with this archaic human population.[4] Modern Western Africans (e.g., Yoruba of Ibadan, Nigeria, Mende of Sierra Leone) may have more ancestry from this lineage as a result of their ancestry from Basal West Africans.[4] [5] The same study also suggests that at least part of this archaic admixture is also present in Eurasians/non-Africans, and that the admixture event or events range from 0 to 124 ka B.P, which includes the period before the Out-of-Africa migration and prior to the African/Eurasian split (thus affecting in part the common ancestors of both Africans and Eurasians/non-Africans).[6] [7] [8] Chen et al. (2020) found that Africans have higher Neanderthal ancestry than previously thought. 2,504 African samples from all over Africa were analyzed and tested on Neanderthal ancestry. All African samples showed evidence for minor Neanderthal ancestry, but always at lower levels than observed in Eurasians.[9]

Even before 300,000 BP to 200,000 BP, when the ancestors of the modern San split from other modern humans, the group to split the most early from modern humans may have been Basal West Africans.[10] Yet, Basal West Africans did not split before Neanderthals split from modern humans.[10]

West African Hunter-Gatherers, Khoisan, and Taforalts

While a less simpler modeling (without Basal West Africans) for the ancestry of the Shum Laka foragers was composed of ancient Taforalts from the Iberomaurusian culture and modern West Africans, among other types of modeling, one modeled the ancestry for the Shum Laka foragers as 65% Basal West African and 35% West African hunter-gatherer from western Central Africa.[11] However, there is an absence of Basal West African ancestry in modern hunter-gatherers of Cameroon.[11]

The peoples of southern Africa (e.g., Khoisan), who are closer in ancestry to peoples of East Africa, are more distant in ancestry to peoples of Western Africa.[1] [2] While contending with the model that supports Southern Africans as the earliest group to split from modern humans, Basal West Africans, as a hypothetical lineage, support two models of equal likelihood – an early basal group from Eastern Africa, which was part of an ancient genetic structure in Africa, are part of the modern ancestry of modern Western Africans (e.g., Yoruba, Mende) or the admixed ancestry of modern Western Africans (e.g., Yoruba, Mende) are the result of early migratory basal groups from different parts of Africa (i.e., Southeastern Africa, Western Africa).[1] [2]

In addition to having similarity with the remnant of a more basal Sub-Saharan African lineage (e.g., a Basal West African lineage shared between Yoruba and Mende peoples),[10] [12] the Sub-Saharan African DNA in the Taforalts of the Iberomaurusian culture may be best represented by modern West Africans (e.g., Yoruba).[12]

Descendants

Yoruba and Mende peoples descend from Basal West Africans and another set of ancestors akin to East Africans and Non-Africans, which is indicative of migration from East Africa.[10] Yoruba people have less ancestry from Basal West Africans than Mende people do,[10] which have a large amount of ancestry.[13] More specifically, Yoruba people have 9% Basal West African ancestry and Mende people have 13% Basal West African ancestry.[3]

Notes and References

  1. Book: Capelli . Cristian . Montinaro . Francesco . Oxford Research Encyclopedia of African History . Genetics and Southern African History . October 24, 2018 . https://ora.ox.ac.uk/objects/uuid:1e7dfa48-725b-43ce-86e4-f0e102e0a0fa/download_file?safe_filename=Capelli_2018_Genetics%252Band%252BSouthern%252BAfrican%252BHistory.pdf&file_format=application%2Fpdf&type_of_work=Book+section . Oxford University Research Archive . 7 . 10.1093/acrefore/9780190277734.013.446 . 978-0-19-027773-4 . 134983982.
  2. Montinaro . Francesco . Capelli . Cristian . The evolutionary history of Southern Africa . Current Opinion in Genetics & Development . 2018 . 53 . 160 . 10.1016/j.gde.2018.11.003 . 30522870 . 54483869.
  3. Web site: Vidal . Gerard Serra . Insights into the human demographic history of Africa through whole-genome sequence analysis . 2018 . Universitat Pompeu Fabra Barcelona . 162 . 108974583.
  4. Durvasula . Arun . Sankararaman . Sriram . Recovering signals of ghost archaic introgression in African populations . Science Advances . 2020 . 6 . 7 . eaax5097 . 10.1126/sciadv.aax5097 . 32095519 . 7015685 . 2020SciA....6.5097D . 211472946 . 2375-2548 . 8538353312.
  5. Book: Sirak . Kendra A. . Sawchuk . Elizabeth A. . Prendergast . Mary E. . Oxford Research Encyclopedia of African History . 18 May 2022 . Oxford University Press . 10–11 . https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/acrefore-9780190854584-e-484%5B1%5D.pdf . Ancient Human DNA and African Population History.
  6. Durvasula A, Sankararaman S . February 2020 . Recovering signals of ghost archaic introgression in African populations . Science Advances . 6 . 7 . eaax5097 . 2020SciA....6.5097D . 10.1126/sciadv.aax5097 . 7015685 . 32095519 . free. "Non-African populations (Han Chinese in Beijing and Utah residents with northern and western European ancestry) also show analogous patterns in the CSFS, suggesting that a component of archaic ancestry was shared before the split of African and non-African populations...One interpretation of the recent time of introgression that we document is that archaic forms persisted in Africa until fairly recently. Alternately, the archaic population could have introgressed earlier into a modern human population, which then subsequently interbred with the ancestors of the populations that we have analyzed here. The models that we have explored here are not mutually exclusive, and it is plausible that the history of African populations includes genetic contributions from multiple divergent populations, as evidenced by the large effective population size associated with the introgressing archaic population...Given the uncertainty in our estimates of the time of introgression, we wondered whether jointly analyzing the CSFS from both the CEU (Utah residents with Northern and Western European ancestry) and YRI genomes could provide additional resolution. Under model C, we simulated introgression before and after the split between African and non-African populations and observed qualitative differences between the two models in the high-frequency–derived allele bins of the CSFS in African and non-African populations (fig. S40). Using ABC to jointly fit the high-frequency–derived allele bins of the CSFS in CEU and YRI (defined as greater than 50% frequency), we find that the lower limit on the 95% credible interval of the introgression time is older than the simulated split between CEU and YRI (2800 versus 2155 generations B.P.), indicating that at least part of the archaic lineages seen in the YRI are also shared with the CEU..."
  7. https://www.science.org/doi/10.1126/sciadv.aax5097 Supplementary Materials for Recovering signals of ghost archaic introgression in African populations", section "S8.2" "We simulated data using the same priors in Section S5.2, but computed the spectrum for both YRI [West African Yoruba] and CEU [a population of European origin] . We found that the best fitting parameters were an archaic split time of 27,000 generations ago (95% HPD: 26,000-28,000), admixture fraction of 0.09 (95% HPD: 0.04-0.17), admixture time of 3,000 generations ago (95% HPD: 2,800-3,400), and an effective population size of 19,700 individuals (95% HPD: 19,300-20,200). We find that the lower bound of the admixture time is further back than the simulated split between CEU and YRI (2155 generations ago), providing some evidence in favor of a pre-Out-of-Africa event. This model suggests that many populations outside of Africa should also contain haplotypes from this introgression event, though detection is difficult because many methods use unadmixed outgroups to detect introgressed haplotypes [Browning et al., 2018, Skov et al., 2018, Durvasula and Sankararaman, 2019] (5, 53, 22). It is also possible that some of these haplotypes were lost during the Out-of-Africa bottleneck."
  8. Durvasula A, Sankararaman S . February 2020 . Recovering signals of ghost archaic introgression in African populations . Science Advances . 6 . 7 . eaax5097 . 2020SciA....6.5097D . 10.1126/sciadv.aax5097 . 7015685 . 32095519.
  9. Chen L, Wolf AB, Fu W, Li L, Akey JM . February 2020 . Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals . Cell . 180 . 4 . 677–687.e16 . 10.1016/j.cell.2020.01.012 . 32004458 . 210955842. free .
  10. Skoglund . Pontus . etal . Reconstructing Prehistoric African Population Structure . Cell . 2017 . 171 . 1 . 59–71.e21 . 10.1016/j.cell.2017.08.049 . 28938123 . 5679310 . 1257429 . 0092-8674 . 7144495602.
  11. Lipson . Mark . etal . Ancient West African foragers in the context of African population history . Nature . 2020 . 577 . 7792 . 668–669 . 10.1038/s41586-020-1929-1. 8386425 . 31969706 . 2020Natur.577..665L . 210862788 . 0028-0836 . 8516105991.
  12. Book: Jeong . Choongwon . The Handbook of Mummy Studies: New Frontiers in Scientific and Cultural Perspectives . Current Trends in Ancient DNA Study: Beyond Human Migration in and Around Europe . https://link.springer.com/referenceworkentry/10.1007%2F978-981-15-1614-6_10-1 . 2020 . 6 . Springer Nature . 10.1007/978-981-15-1614-6_10-1 . 978-981-15-1614-6 . 226555687 . 1182512815.
  13. Wonkam . Ambroise . etal . Exome sequencing of families from Ghana reveals known and candidate hearing impairment genes . Communications Biology . 2022 . 5 . 1 . 369 . 10.1038/s42003-022-03326-8 . 35440622 . 9019055 . 9478623435 . 248264573.

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