Did Niger-Congos came about as a fusion of "NE African"-like and Khoisan/"Pygmies"?

[Muslim-Arbegna]

It's seems that all the evidence of the genetics of SSA Niger-congos as being a fusion of NE African-like people (likely males) and Khoisan like (or something similar).

That fact that Niger-Congos are in the mid point between NE Africans and HGs. And their haplogroup is overwhelmingly of E among males (of NE African origin) and their mtdna is L0 similar to most khoisans. The last thing is their "phenotype", I know "phenotype" is little dubious, their hair texture is a fusion of NE African and Khoisan, as Khoisans have very short "popcorn" hair, while NE African is tight curly to Wavy, while the hair of the of SSA niger-Congos is somewhat similar to NE African in texture than to a khoisan, but it's short like HG's.

[Muslim-Arbegna]

I they were either majority NE Africans and part Basal Human or just NE African + Khoisan/Pygmies.

[NetNomad]

I don't think so. Wasn't this some silly theory of Carleton Coon or the like?

More likely they seem like a paleolithic-era split from East Africans with some minor local admixture (archaic as well as AMH). The upcoming Shum Laka paper may clarify the situation when it is published.

[Piquerobi]

This is from a 2017 study. Hopefully newer studies - including ancient remains being tested - will be published soon.

We carried out admixture graph modeling of the allele frequency correlations and found two parsimonious models that fit the data. The first posits that present-day western Africans harbor ancestry from a basal African lineage that contributed more to the Mende than it did to the Yoruba, with the other source of western African ancestry being related to eastern Africans and non-Africans (Figures 3D, S4, and S5; Table S7). The second model posits that long-range and long-standing gene flow has connected southern and eastern Africa to some groups in western Africa (e.g., the ancestors of the Yoruba) to a greater extent than to other groups in western Africa (e.g., the ancestors of the Mende) (Figure 3E) (Pleurdeau et al., 2012). The possible basal western African population lineage would represent the earliest known divergence of a modern human lineage that contributed a major proportion of ancestry to present-day humans. Such a lineage must have separated before the divergence of San ancestors, which is estimated to have begun on the order of 200–300 thousand years ago (Scally and Durbin, 2012). Such a model of basal western African ancestry might support the hypothesis that there has been ancient structure in the ancestry of present-day Africans, using a line of evidence independent from previous findings based on long haplotypes with deep divergences from other human haplotypes (Hammer et al., 2011; Lachance et al., 2012; Plagnol and Wall, 2006). One scenario consistent with this result could involve ancestry related to eastern Africans (and the out-of-Africa population) expanding into western Africa and mixing there with more basal lineages.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679310/

African2017d.f.787272Capture1.png

[Brwn_trd]

It's seems that all the evidence of the genetics of SSA Niger-congos as being a fusion of NE African-like people (likely males) and Khoisan like (or something similar).

That fact that Niger-Congos are in the mid point between NE Africans and HGs. And their haplogroup is overwhelmingly of E among males (of NE African origin) and their mtdna is L0 similar to most khoisans. The last thing is their "phenotype", I know "phenotype" is little dubious, their hair texture is a fusion of NE African and Khoisan, as Khoisans have very short "popcorn" hair, while NE African is tight curly to Wavy, while the hair of the of SSA niger-Congos is somewhat similar to NE African in texture than to a khoisan, but it's short like HG's.

I am very curious about this as well. The greatest diversity in Y chromosome and language are in far west africa, Senegal, Gambia Guinea but genetically there are two genetic components. These are a Bantu component and a West African component. The components are not very different. Could Bantu be autosomally local with Y chromosome from the west? Mtdna is more spatially structured compared to Y chromosome which are more homogeneous. How these populations relate to other Africans is also a mystery. Looking forward to ancient dna although this is not likely. Very few skeletal remains have been obtained from west Africa. Those from Nigeria (Itaakpa) at the turn of the age are similar to Shum laka which is now claimed to be more like Central African Hunter gatherers than Niger Congo speakers! Can’t wait

[Angoliga]

This is from a 2017 study. Hopefully newer studies - including ancient remains being tested - will be published soon.


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679310/

African2017d.f.787272Capture1.png

I tend to favor this more recent model from Lazardis' (2018):

 

.. our model predicts that West Africans (represented by Yoruba) had 12.5%±1.1% ancestry from a Taforalt related group rather than Taforalt having ancestry from an unknown Sub-Saharan African source; this may have mediated the limited Neanderthal admixture present in West Africans.

This model takes the Iberomaurusian samples into account and supports other independent observations relating to archaic introgression in modern West-Africans (Durvasula, 2019):

While introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. Using 405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to 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 that recover about 482 and 502 megabases of archaic sequence, respectively. 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 African populations.

This range using G25 seems to hold ground with ancient North-African (MAR_Iberomaurusian) and archaic SSA (MWI_Fingira_2500BP) against modern West-Africans:

[1] "distance%=28.0652"

         Mende_Sierra_Leone

MWI_Fingira_6100BP,63.7
MWI_Fingira_2500BP,16.3
MAR_Iberomaurusian,15.2
MAR_EN,3.8
Anatolia_N_Kumtepe_low_res,0.4
RUS_Ust_Ishim,0.3
CHN_Tianyuan,0.1
Jarawa,0.1
VNM_BA_all,0.1

1] "distance%=31.1751"

         Esan_Nigeria

MWI_Fingira_6100BP,67.1
MAR_Iberomaurusian,15.5
MWI_Fingira_2500BP,12.4
MAR_EN,4.1
RUS_Ust_Ishim,0.4
Anatolia_N_Kumtepe_low_res,0.4

[1] "distance%=29.943"

         Igbo

MWI_Fingira_6100BP,69.5
MAR_Iberomaurusian,16
MWI_Fingira_2500BP,10.9
MAR_EN,3.3
Anatolia_N_Kumtepe_low_res,0.3

[1] "distance%=31.2193"

         Yoruba

MWI_Fingira_6100BP,70.6
MAR_Iberomaurusian,15.8
MWI_Fingira_2500BP,8.5
MAR_EN,4.7
BLZ_SakiTzul_7400BP,0.2
CHL_LosRieles_5100BP,0.1
Anatolia_N_Kumtepe_low_res,0.1



[1] "distance%=28.1667"

         Gambian

MWI_Fingira_6100BP,68.7
MAR_Iberomaurusian,19
MWI_Fingira_2500BP,7.3
MAR_EN,4.6
Anatolia_N_Kumtepe_low_res,0.3

[1] "distance%=28.2958"

         Mandenka

MWI_Fingira_6100BP,69.6
MAR_Iberomaurusian,19.6
MWI_Fingira_2500BP,6.4
MAR_EN,4
Anatolia_N_Kumtepe_low_res,0.2
BLZ_SakiTzul_7400BP,0.1
PER_Laramate_900BP,0.1

- there's a separate thread with an even wider range of Africans; though admittedly, it was very amateurishly presented.

More on the Durvasula paper's period of introgression are discussed here.

It's provisionally stated but according to the paper's model, ancestry of this unknown hominin is also shared with non-Africans:

...We observe that the CEU CSFS, like the CSFS in the African populations, is U-shaped with an increase in the counts of high frequency alleles. (Figures S4 and S6). Further, we also observe a U-shape in the CSFS computed in the Han Chinese/CHB population (Figure S6). These results suggest that a component of the archaic ancestry that we detect in African populations is shared with non-African populations. We view these results as provisional and additional detailed modeling needs to be done to resolve the history and timing of archaic introgression.”

... can't wait to see what comes out the Shum Laka samples!

[Muslim-Arbegna]

I don't think so. Wasn't this some silly theory of Carleton Coon or the like?

More likely they seem like a paleolithic-era split from East Africans with some minor local admixture (archaic as well as AMH). The upcoming Shum Laka paper may clarify the situation when it is published.

No, not at all. This is just an observation.

[BrendaAnderson]

Oh, that was nice.