A research paper published by Fan et al., in Cell, in 2023 reported their findings regarding genetic diversity in Africa, as well as suggesting archaic introgression of very divergent ancestors into all humans, in Africa, and also a recent introgression into some specific populations.
This is the paper: Fan S,. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell. 2023 Mar 2;186(5):923-939.e14. doi: 10.1016/j.cell.2023.01.042. PMID: 36868214; PMCID: PMC10568978.
Introgression
There are two populations that stand out in their analysis. One is the Tikari, from the Tropical jungles of Cameroon in Western Africa, the other are the Herero, from Botswana, the same region where the Ju|’hoansi and !Xoo, San or Khoisan people, come from. The authors note that they have up to 23% of a divergent archaic genetic content, that is olver than the split of all modern humans (highlight is mine):
"The relationship of the Tikari and Herero with other populations is complex. They could be modeled as having 23% ancestry related to an archaic population that diverged prior to the divergence of all modern human populations (possibly reflecting introgression from an archaic population into modern populations) and 77% ancestry from a population related to the Nilo-Saharan-speaking Mursi. A similar pattern was observed in the ADMIXTURE analyses at K = 7 to 11 but with much lower inferred Nilo-Saharan-related ancestries in the Tikari and Herero (Figure S2). The TreeMix analyses showed evidence of gene flow between the Mursi and the ancestors of the Tikari and Herero starting at 5 migration events (Figure S3F). The results indicating archaic introgression in a population ancestral to the Bantu-speaking lineage are consistent with previous studies based on ancient African samples which suggested that the West African Niger-Congo-speaking populations carry lineages ancestral to all modern human lineages. However, time-resolved demographic history models inferred using alternate methods (described below) suggest that the ancestors of San and RHG may have been the first to split from other modern human lineages."
The gene flow from Mursi, an East African group from Ethiopia into West Africa is remarkable. Notice how the quote ends with a comment stating "yes, they may have archaic introgression, but, other methods show that the San are part of the oldest human lineage.
This ancient group, the archaics, split from us 1 to 3 million years ago. But, the authors also suggest an alternate explanation: structured populations. Isolated groups of humans exchanging alleles every now and then would produce the same effect as a ghost introgression:
"Across all pairs of populations, we inferred that all modern humans descend from deeply structured populations and that they derive approximately 5–15% of their ancestry from a lineage that may have diverged as long ago as 1–3 Mya (Figure 4C), consistent with previous findings suggesting archaic introgression in some African populations.However, such a model is also consistent with the population ancestral to modern humans being deeply structured."
They paint a complex scenario with "multiple episodes of gene flow between modern human lineages and possibly with other hominid lineages"
Below is a tree showing the splits and archaic introgressions (San on the right, non-Africans, left. Africans in between).
Pale Skin, shared by San and Europeans
As discussed in a previous post, San and non-Africans share a variant linked to pale skin pigmentation. This paper reports that "rs1800404, a synonymous variant in exon 10, associates with skin pigmentation and eye color variation across multiple ethnicities. The light-pigmentation associated allele rs1800404-T, which is a splicing QTL of OCA252,58, is most frequent in the San (83%) compared to all other populations in the present study and gnomAD except for the Finnish population (frequency of 84%)." The supplementary material table S4 shows the frequencies in different populations as follows: Starting with African populations, and ending with the gnomAD ge nome database that gives general values for AFR (Africans), AMR are Latino-Admixed American. ASJ: Ashkenazi Jews. EAS: East Asian. FIN: Finns. NFE: non-Finnish Europeans, and OTH: unclassified, residual groups.
Amhara 37%
RHG 10%
Dizi 10%
Fulani 23%
Hadza ~0%
Herero ~0%
Ju|'hoansi 83%
Mursi 7%
Chabu 0%
Sandawe 23%
Tikari 0%
!Xoo 83%
gnomAD_genome_AFR 21%
gnomAD_genome_AMR 56%
gnomAD_genome_ASJ 71%
gnomAD_genome_EAS 39%
gnomAD_genome_FIN 83%
gnomAD_genome_NFE 80%
gnomAD_genome_OTH 73%
This seems a strange trait, absent in all of Africa (where dark pigmentation prevails, but present in San and all non-Africans. Note that ALL non-Africans have higher values than Africans except the San Koisan people. The Amhara of Ethiopia, have according to the paper "experienced strong non-African admixture (e.g., Amhara from Ethiopia)"
The paper goes on to descibe another allele, PDPK1, studying different SNPs along it, and noting that it regulates skin pigmentation (reducing the growth of skin-coloring cells called melanocytes, in mice). At one of the SNPs, rs77665059, the ancestral variant "C" (cytosine) is found at higher frequencies among the San people (67 to 83%) vs. other African groups (3%) and non-Africans (14%). "Individuals with the C allele have lighter skin pigmentation compared to individuals with the A allele in the San." Unfortunately, there is no data table to show its frequency in different populations. But from online databases, I prepared the following table (Source and Source)
Population C (derived allele)
Group frequency
Total Global 1.81%
European 0.75%
Azkhenazi Jews 1.03%
African 9.63%
African Others 10.5%
African American 9.6%
Asian 0%
East Asian 0%
Other Asian 0%
South Asian 0%
Latin American 1 3.3%
Latin American 2 1.21%
Other 1,88%
This is clearly a San, and African trait. Possibly originating from the ancestral archaic hominins. I would suggest that the high prevalence among some Latin Americans is due to the slave trade, that incorporated African genes into admixed Amerindian populations.
Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall ©
