In a recent post I wrote about the Neutral Theory of molecular genetics, and its shortcomings. Today's post will explore the African genetic diversity, a foundation on which the Out Of Africa (OOA) theory is based.
There are several questions that should be answered: Do modern Africans reflect the genetic makeup of ancient Africa 100,000 or 75,000 years ago? Is a modern Nigerian, Gambian, Angolan African representative of the ancient population from which the Out of Africa migrants split? Have other events taken place within Africa in other populations that were isolated from the sub-population that was the root or base from which modern H. sapiens migrated into Eurasia?
Admixture with archaic hominins after the OOA event (such as H. naledi), admixture between many separate and formerly isolated hunter gatherer sub-populations due to migrations like the Bantu migration could have led to a modern highly diverse African population, while the original OOA root was far less diverse.
The image below is a crude attempt to reflect the isolated populations within Africa at the time modern Humans appeared. Each circle is a population. They all contain allelles (colored red, blue, yellow, etc.) some shared, others unique to each population. The black arrows show the migration Out of Africa, with humans dispersing across Eurasia towards Siberia, Europe and Oceania, and America. They lose diversity on the way due to Genetic Drift.
The dashed red arrows converging on a circle shows the internal migrations within Africa by which these formerly isolated sub-populations of humans admixed and the final, contemporary population has an even higher diversity than the original root of the Out of Africa migration (set in the horn of Africa).
It does not show any back-flow of humans from Eurasia into Africa, or archaic introgression either in Africa or in Eurasia (Neanderthals, Denisovans).
Population structure in Africa
The humans in Africa were not a uniform population. A paper published in Nature suggested that there were "low levels of gene flow among archaic populations before the emergence of anatomically modern humans — that is, they imply the existence of ancestral population structure." It also hints at admixture with primitive, archaic, hominins in Africa: "There is also growing evidence that some highly divergent genetic lineages might have entered our genome through hybridization between an expanding anatomically modern human population and archaic forms of humans."
Another article published in Nature, questions the use of modern Africans to model the OOA event. While highlighting the high diversity within Africa, the paper also states that "we will need to establish whether selection has continued to operate effectively on complex traits, leading to unbiased estimates from these populations. If not, it may still be inappropriate to use a specific modern African population as a proxy for the ancestral population of modern humans."
Additional research (Source) looks into the effects of the structured population within ancient pre-OOA Africa: "Several studies have indicated that ancestral populations were geographically structured before modern humans migrated out of Africa. For example, it has been suggested that the deep coalescence times of mtDNA and X-chromosome lineages are consistent with a demographic scenario of ancient population structure in Africa. A recent analysis of cranial shape variability in anatomically modern human fossils (dating to 200–60 kya) from Africa and the Middle East also reported a high level of morphological divergence among these fossil hominids which was interpreted as evidence for ancestral population structure in Pleistocene Africa. Thus, arguably, a considerable amount of genetic and phenotypic diversity may have been present at an early stage of modern human evolution."
Indeed! And not all of this diversity was found in one population, each sub-population had their own alleles, later admixed into modern Africans (minus alleles lost due to genetic drift) and plus backflow from Eurasia with introgressed Neanderthal genes, and the mutations added by an additional 100 ky of evolution in Africa, subjected to natural selection and random mutations over that period of time.
This paper also mentions the backflow: "The reverse migration of non-Africans into Africa was also shown to contribute to the gene-pool of modern African populations"
The variations observed in skulls mentioned above was reported by a paper published in Nature. Different skull shapes mean that different sets of genes were working and they were not the same alleles in each sub-population.
"Late Middle Pleistocene (LMP, from 350 to 130 ka) African fossils [were highly variable]... Even when excluding the H. naledi material, African LMP fossils exhibit extremely variable morphologies. The Omo I22 and Herto specimens have a modern-like anatomy... and are generally considered the earliest undisputed remains of H. sapiens. All other LMP African fossils show a mosaic of derived and archaic characters. For instance, the Jebel Irhoud remains were originally described as showing strong similarities with Neandertals, while the study of the new Irhoud remains emphasises their affinities with H. sapiens, despite the absence of key modern humans apomorphies. The Guomde, Ngaloba, Eliye Springs and Florisbad specimens along with Omo II... have been mostly referred to as ‘archaic H. sapiens’, a category grouping isolated fossils with disparate morphologies. This situation challenges any attempt at identifying the evolutionary mechanisms that may explain the morphological pattern in the African LMP fossil record, as well as identifying the ancestral population, or populations, of modern humans"
The Admixture Within Africa
These different groups of humans must have later admixed into the base from which modern Africans come from. Possibly after the basal Homo sapiens left Africa in its OOA journey.
Yet another paper from Nature investigated contemporary African diversity. It looked at the genes and ancient migrations in different populations, including the Hunter gatherers (HG) and the supposedly most ancient group of humans, and the most diverse one, those living in sub-Saharan Africa (SSA), to define the current genome of Africans. It found an important effect from Eurasian admixture and a strong influence of natural selection modelling modern genes:
"Eurasian ancestry has a substantial impact on differentiation among SSA populations...
We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA. Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; ∼7,500–10,500 years ago), old admixture among Ethiopian populations (∼2,400–3,200 years ago) consistent with previous reports, and more recent complex admixture in some East African populations (∼150–1,500 years ago). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period.
We also find evidence for complex and regionally distinct HG admixture across SSA, with ancient gene flow (∼9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations.
Positive selection in SSA
We examined highly differentiated SNPs between European and African populations, as well as among African populations to gain insights into loci that may have undergone selection in response to local adaptive forces. To account for confounding due to Eurasian admixture, we also conducted analyses after masking Eurasian ancestry. On examining locus-specific Europe–Africa differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.4 × 10−31). Furthermore, there was statistically significant enrichment for gene variants among these, indicating that this differentiation is unlikely to have arisen purely from random drift..."
So modern African diversity is the result of recent admixture across the continent and the forces of natural selection. These people are not the same people that saw the OOA migration depart.
Archaic introgression in Africa
Regarding introgression of archaic human in Africa, I had posted back in 2019 about it (See post: Archaic Ghost population admixed with Modern Humans in Africa) which quotes a paper by Lorente-Galdos et al. that reported that: "We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage."
Another paper form 2020, published in Science found the same effect in Western Africa: "We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations."
This introgression took place in West Africa after the OOA: "the admixture time ... 43,000 years B.P. (95% HPD: 6000 to 124,000), and the admixture fraction ... 0.11 (95% HPD: 0.045 to 0.19).", that is 11% mean (4.5 to 19%). And then subject to selection as it was an adaptive introgression.
This surely contributed to the diversity of the alleles in these people compared to those who left Africa in the OOA migration.
Other confounders
Finally, there is the question of back-migrations from Eurasia into Africa. These people who returned "Into Africa" or "Out of Asia" back flow carried with them genes from people who had left Africa, plus admixture with Neanderthals (and maybe, Denisovan, ultra-archaics, first wave humans who left before the final OOA event). This surely contributed to the genetic diversity of Africa.
Another element to consider is the mutation speed or faster evolutionin Africa which could have fueled diversity starting even before the final OOA event 60-100 ky ago. But that is the subject of a future post.
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