Did the Bantu expansion really occur?

[djoser-xyyman]

Been away awhile also on the other site. But ESR remains where I post my best material.

That said here is something new on the Bantu Expansion. from my post on ESR

gbe.oxfordjournals.org/content/7/9/2560.full.pdf


This work seems to a refute the work by - (Sikora M. 2011. A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations. Eur J Hum Genet. 19:84–88.) which debunks the Bantu hypothesis.


I will look into this new paper. This Busby guy seems to be making a name for himself. He co-authored.

[djoser-xyyman]

This is the paper from Calafel, Comas and Sikora

A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations - Martin Sikora, , Francesc Calafell, David Comas and Jaume Bertranpetit*


Abstract
Studies of large sets of single nucleotide polymorphism (SNP) data have proven to be a powerful tool in the analysis of the genetic structure of human populations. In this work, we analyze genotyping data for 2841 SNPs in 12 sub-Saharan African populations, including a previously unsampled region of southeastern Africa (Mozambique). We show that robust results in a world-wide perspective can be obtained when analyzing only 1000 SNPs. Our main results both confirm the results of PREVIOUS studies, and show new and interesting features in sub-Saharan African genetic complexity. There is a strong differentiation of Nilo-Saharans, much beyond what would be expected by geography. Hunter-gatherer populations (Khoisan and Pygmies) show a clear distinctiveness with very intrinsic Pygmy (and not only Khoisan) genetic features. Populations of the West Africa present an unexpected similarity among them, possibly the result of a population expansion. Finally, we find a strong differentiation of the southeastern Bantu population from Mozambique, which suggests an assimilation of a ****pre-Bantu substrate**** by Bantu speakers in the region.

European Journal of Human Genetics (2011) 19, 84–88; doi:10.1038/ejhg.2010.141; published online 25 August 2010

[djoser-xyyman]

As a reminder -
This from the Sikora paper
Quote:

The southeastern Bantu from Mozambique are remarkably differentiated from the western Niger-Congo speaking populations, such as the Mandenka and the Yoruba, and also differentiated from geographically closer Eastern Bantu samples, such as Luhya. These results suggest that the Bantu expansion of languages, which started B5000 years ago at the present day border region of Nigeria and Cameroon, and was probably related to the spread of agriculture and the emergence of iron technology,17–19 was ****NOT***** a demographic homogeneous migration with population replacement in the southernmost part of the continent, but acquired more divergence, likely because of the integration of pre-Bantu people. The complexity of the expansion of Bantu languages to the south (with an eastern and a western route20), might have produced differential degrees of assimilation of previous populations of hunter gatherers. This assimilation has been detected through uniparental markers because of the genetic comparison of nowadays hunter gatherers (Pygmies and Khoisan) with Bantu speaker agriculturalists.2,21–24 Nonetheless, the singularity of the southeastern population of Mozambique (poorly related to present Khoisan) could be attributed to a complete assimilation of ancient genetically differentiated populations (presently unknown) by Bantu speakers in southeastern Africa, without leaving any pre-Bantu population in the area to compare with.

[djoser-xyyman]

What Sikora is saying is this ancient population whose genetic material is found in South East Africa is NOT related to the Khoisan who is another African population.

All the answers are @ K5 in Fig S5. Does it contradict what the author is suggesting?

BTW - this is one of many studies that confirm that the Juhoansi A/B seems to be the “purest” or oldest African population.

[djoser-xyyman]

I am not sure what Busby and his buddies are saying here. Sikora et al never stated that the pre-Bantu element was

1. Restricted to Mozambique
2. FROM the modern day hunter gatherers. As stated about Sikora this ancient genetic material was POORLY related to Khoisan. ie it was NOT Khoisan. Sikora stated – the source is presently unknown.

Am I missing something? Anyone? Seems like Busby is attacking Sikora without any basis. ie Is Busby a strawman?

------

Quote:

To test these hypotheses and further characterize the reported Mozambican component, we analyzed new genomewide single nucleotide polymorphism(SNP) array data from 35 sub-Saharan African populations from 868 individuals (including 33 novel genotypes from Namibia and Lesotho) (fig. 2). Our results place the so-called “South-Eastern component” within the broader genetic variation of Southern Africa. Additionally, we find no evidence in the Mozambican population for substantial gene flow between Bantu and HUNTERGATHERER POPULATIONS **FROM ***this region.

Results
Relationships among individuals were explored using principal component analysis (PCA) (fig. 3). The first component (PC1) shows a separation of Khoisan-speaking groups from the other populations, with East non-NC populations separating along the second component (PC2) (fig. 3a). To further analyze these results, a second PCA was performed removing the East non-NC (Afro-Asiatic, Nilo-Saharan, and linguistic isolates) populations. In this, the Khoisan-speaking groups and the NC-speaking populations are separated along the first component (PC1), the rainforest hunter-gatherers (RHG, also known as Pygmies) located among the two (fig. 3b). RHG are separated from the other populations along the second

-------


Sikora clearly stated it was NOT from the Hunter gathers.

[djoser-xyyman]

Looks like Busby and Co are now attacking Sikora and me. They are attacking the theory that the Bantu expansion did not occur by creating a strawman argument.

[djoser-xyyman]

Again to clarify; this is what Gonzales-Santos/Busby et al ..VERSUS ..Sikora et al states. Santos/Busby is arguing that this “genetic material” found is Mozambicans is widespread in “southern Africa” and is NOT FROM the Hunter gathers. Sikora never said it was. Lol!



=======
Quote from Santos/Busby:
To test these hypotheses and further characterize the reported Mozambican component, we analyzed new genomewide single nucleotide polymorphism(SNP) array data from 35 sub-Saharan African populations from 868 individuals (including 33 novel genotypes from Namibia and Lesotho) (fig. 2). Our results place the so-called “South-Eastern component” within the broader genetic variation of Southern Africa. Additionally, we find no evidence in the Mozambican population for substantial gene flow between Bantu and HUNTERGATHERER POPULATIONS FROM this region.



But this is what Sikora et al states

Quote:

The southeastern Bantu from Mozambique are REMARKABLY ***differentiated*** from the western Niger-Congo speaking populations, such as the Mandenka and the Yoruba, and ALSO differentiated from geographically CLOSER Eastern Bantu samples, such as Luhya. These results suggest that the Bantu expansion of languages, which started 5000 years ago at the present day border region of Nigeria and Cameroon, and was probably related to the spread of agriculture and the emergence of iron technology,17–19 was ****NOT***** a demographic homogeneous migration with population replacement in the southernmost part of the continent, but acquired more divergence, likely because of the integration of pre-Bantu people. The complexity of the expansion of Bantu languages to the south (with an eastern and a western route20), might have produced differential degrees of assimilation of previous populations of hunter gatherers. This assimilation has been detected through uniparental markers because of the genetic comparison of nowadays hunter gatherers (Pygmies and Khoisan) with Bantu speaker agriculturalists.2,21–24 Nonetheless, the singularity of the southeastern population of Mozambique (poorly related to present Khoisan) could be attributed to a complete assimilation of ancient genetically differentiated populations (presently unknown) by Bantu speakers in southeastern Africa, without leaving any pre-Bantu population in the area to compare with.

========

Clearly a strawman. I expect a rebuttal from Sikora. Sikora is stating the South Eastern Bantus has more variation than the Western Bantus. In other words they are older. He “interprets” this genetic signature as an OLDER African population NOT related to Khoisan somehow admixed the Bantus. Archeology vs Genetics?

[djoser-xyyman]

Let’s dig into this further. So. Sikora et al observed specific genetic material IN the South East Bantus that was NOT observed in Western Bantus like Yoruba. His explanation?! There was a “pre-Bantu” population in South Eastern Africa that got “assimiliated” by the incoming Bantus. He assumes this population no longer exist or haven’t been tested as yet. They were NOT the Khoisans.

The problem is he is assuming all “Bantus” are related based upon what he “read” in the archeology books.

Now let us look at what Santos/Busby did. Like Sikora they also confirmed that there is no South East Bantus/Khoisan admixture(they attributed that Sikora wink! Wink!), They also agreed that there is marked DIFFERENCES between South East Bantus and Western Bantus. They are two different groups. Now the East/Central African Bantus(Luyha) seems to be not really related to these Mozambicans also. These Luhya types peoples are “inbetween” both West and South East Bantus groups. At k6. Now, Santos/Busby chose the green component ONLY to come to their conclusion. Earlier they stated that the “Red” cluster has high frequency in the West and the “Green’ cluster has high frequency in the South East and through out southern Africa. Looking at the Red and Green clusters clearly west and South East are two different groups that may have been isolated for 10’s of thousand of year.


Nevertheless also, keep in mind also Santos-Busby chose ONLY 100SNPs to discredit Sikora et al.

Illustration to come. But look at Supplementals at K6 in the charts.


The red cluster was ignored. All populations in the dataset carry all colors…..except may be the Johuansi population.

[djoser-xyyman]

So there you have it. Santos/Busby just confirmed what Sikora hypothesized. Sikora dataset was restricted to Mozambique and a few other SSA population. Now with the extended dataset by Santos/Busby this genetic component seems to extend into Southern Africa but NOT West Africa. The Geographic pattern as seen at K6, is consistent with that. Green Component has high frequency in Mozambique and East areas into South Africa and decreases to the West. The “red” component has high frequency in West Africa and decreases to the East. This basically confirms that West African Bantus and East/South West Bantus are ‘different’ irregardless of the similar features. East Africans are NOT a subset of West Africans as the popularly believed.


What is more interesting from the study looking at figS5 chart is at K3. Anyone notice the light purple component has highest frequency in Great Lakes population and present but drops off in West African Bantus. But virtually absent in South-East African Bantus and Click Speakers (except Hadza/Sandwe). If I am a betting man that is the Neolithic genetic material. Remember Hadza/Sandwe have more “Eursasian” labeled genetic material than the heavily admixed African-American. Tic! Toc!




Quote:
In the second component of the PCA, Mozambique appears as part of a cluster of several sub-Saharan African populations speaking NC languages and distributed along a Northeast–Southwest continuum (fig. 3b). The ADMIXTURE components present in the Mozambican samples are the same as those of other East and South-Eastern African populations from Kenya, South Africa, and Lesotho (fig. 4a).

[djoser-xyyman]

Rasol back then did not have the evidence/data we have today. The data shows, yes, Bantus are related but one is NOT a subset of the other. This doge-podge as you put it may be the source and NOT the recipient. Notice the green component increases from the “hodge-podge’ areas to the South East and South West. Wheile the “red” component also increases from the “hodge-podge’ areas to the West. This is consistent with E1b1a originating in N East Africa and dispersing West and South East/South. Other studies cited in this thread based upon larger chunks of genetic material has confirmed South East Bantus are older. Which would make sense.


This will also support what imhotep06 is saying based upon linguistics.

It is critical how the genetic data is interpreted and read..

Jan 17, 2015 20:15:04 GMT -5 Tukuler al~Takruri said:

Ever since I read about the 'expansion'
not being demic as much as "lingo-tech"
in the unabridged UNESCO (it was edited
out of the paperback reprint and even in
the original the co-author of that chapter
and editor of that volume distanced themselves
from the opinion of a born East African BaNtu
historical linguist) I have doubted the 'demic
expansion' though most every other ES OT, even
Rasol a South African, agreed with it and the
earlier reports that supported that theory.

Sikora is sloppy in places and the data
is only SNP based but his STRUCTURE at
K=5 clearly shows BaNtu speakers are of
distinct separate genetic lineages

* northern E Afr Luhya - orange
* southeast Afr Mozambiqans - violet
* south Afr Soweto/Jo-burg- orange + hodgepodge





He proved his ~3k SNPs in PCA analysis
are roughly as good as ~500k SNPs and
thus cost effective for investment
limited researchers. But something
appears off as both sets of genome
samples place many Mexicans in the
Central Asian cluster.

[djoser-xyyman]

imhotep06. So Mboli was correct

[djoser-xyyman]

This carraborates


Quote:
In the second component of the PCA, Mozambique appears as part of a cluster of several sub-Saharan African populations speaking NC languages and distributed along a Northeast–Southwest continuum (fig. 3b). The ADMIXTURE components present in the Mozambican samples are the same as those of other East and South-Eastern African populations from Kenya, South Africa, and Lesotho (fig. 4a).


THIS!




Notice the NorthEast-SouthWest cline



Bantus expansion? – more BS from Europeans

[Tukuler al~Takruri]

Jan 17, 2015 20:15:04 GMT -5 Tukuler al~Takruri said:

Sikora is sloppy in places and the data
is only SNP based but his STRUCTURE at
K=5 clearly shows BaNtu speakers are of
distinct separate genetic lineages

* northern E Afr Luhya - orange
* southeast Afr Mozambiqans - violet
* south Afr Soweto/Jo-burg- orange + hodgepodge

Oct 28, 2015 9:04:19 GMT -5 djoser-xyyman said:

This doge-podge as you put it may be the source and NOT the recipient. Notice the green component increases from the “hodge-podge’ areas to the South East and South West. Wheile the “red” component also increases from the “hodge-podge’ areas to the West. This is consistent with E1b1a originating in N East Africa and dispersing West and South East/South. Other studies cited in this thread based upon larger chunks of genetic material has confirmed South East Bantus are older. Which would make sense.



It is critical how the genetic data is interpreted and read..

Don't know why you drag me into this
but my "hodge-podge" use refers to the
colors in the Soweta/Jo-berg population
of South Africa labeled Bantu at chart's
bottom. Sikora shows them as a hodge-podge
of all five color / K groups of the report.
There is no color distinquishing South Africans.

Repeat: The sampled South African SNPs show
these S.Afrs have predominant "Luhya" ethnic
biology but do include biology from the report's
* general African
* Nilo-Saharan Maasai
* Hunter Gatherers
* Moçambiqans
when it's set to show K=5 distinct breeding populations.

Of course the green (Hunter Gatherers) would
be more numerous in S.Afr since that geography
is the non-baNtu speaking San (so-called bushman)
homeland since before the Khoe migrated south from
Ethiopia. These people's language is also not of
Niger-Congo -- as is baNtu -- but a superphylum
of its own, Khoisan (Click).

Red represents another non-Bantu non-NigerCongo
language family. It's the Nilo-Saharan speaking
Maasai. The Maasai biological component of the
Luhya is the highest, reflecting East Africa specific
genetics. It does not increase but remains about
the same in S.Afr since it's just a rider within
the E.Afr Luhya element.

The 3 colors orange & red and green show demic
biology infusion from E.Afr to S.Afr i.e., the
NE - SW movement as in your unsourced map.

One conclusion I make is that since neither Khoisan
nor NiloSaharan is the language source for baNtu, a
NigerCongo language, the "E.Afr Luhya"'s general Africa
or NigerCongo biological component is responsible for
baNtu language in S.Afr but that Moçambiqans adopted
the language from interaction with "E.Afr Luhya"-like
population(s) that moved south from East Africa more
likely than "E.Afr Luhya"-like folk moving northeast
from South Africa. This is all in regard to Sikora's
report and not a blanket statement which would require
synthesis from analyses of numerous similar reports.

My adapted chart stops at K=5 populations but we have
no way of knowing at which K the Soweto/Jo-burg baNtu
would emerge as a local breeding population. Sikora
goes up to K=7 w/out S.Afr Bantu becoming distinct.

Moçambiqans emerge as a distinct local breeding population
at K=4, the Luhya at K=5. At K=4 the Luhya are just showing
to be composed of various East African biological groups
only coming into its own at next K level.

Here below please see Sikora's original chart

[djoser-xyyman]

My bad . The hodge-podge I am referring to is in the new Santos /Busby paper. I know you don't like dumbing things down and prefer to look up the image yourself. But I will post for the newbies. The new data show Luyha and other great Lakes Africans being a hodge podge. They are either recipients or the source. I will illustrate later.

[Tukuler al~Takruri]

ok