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Angela
06-06-17, 22:34
See:
http://biorxiv.org/content/early/2017/06/05/145409

Carina M Schlebusch,et al
"Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago"

"Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region's human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|'hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) 'hot spot' for the evolution of our species."

So, do they actually mean that there was no admixture from 260,000 years ago to less than 2,000 years ago. Amazing if true.

I1a3_Young
06-06-17, 23:24
So, do they actually mean that there was no admixture from 260,000 years ago to less than 2,000 years ago. Amazing if true.

Yeah I did a double take when I read that. That is astounding for a population in southern Africa. Could they have been cutoff by a desert or something for a lot of that time?

I1a3_Young
06-06-17, 23:41
I wonder, to what extent can a population change in 100k years of isolation with no admixture.

Angela
07-06-17, 00:41
Even their y is about 160,000 years old, which is extraordinary (A1b1b2). So, from that and other evidence we already knew that the ancestors of the Khoi population and all other populations on earth split 160,000 years ago, so this is effectively "just" pushing it back about 100,000 years. I haven't looked at all the calculations so I don't know if that's accurate, but 160,000 years is plenty long enough for a wow factor already. :)

Another interesting thing for me is that even the San hunter-gatherers who have not adopted the lifestyle of the farmers/pastoralists around them have a small but still significant amount of "new" dna.

The gene flow went the other way too, from other papers

LeBrok
07-06-17, 04:42
Amazing. Has the split happened before Homo Sapiens Sapiens came to existence? Archaic San people might need new classification. ;)

berun
07-06-17, 07:22
Another fiasco, now related to the Khoisans.

bicicleur
07-06-17, 07:57
Yeah I did a double take when I read that. That is astounding for a population in southern Africa. Could they have been cutoff by a desert or something for a lot of that time?

the equatorial forest was a boundary where only specialised pygmee tribes lived
the cattle of the pastoralist tribes didn't survive in warm and moist climate because of diseases caused by the tsee-tsee flies
that held the pastoralists in northern Africa
untill some dry spell allowed them to bypass the equatorial forest on the eastern side

the haplo A Koi and San are the original HG, they speak 'click'-language
the haplo E-M2/V95 Bantu speakers are the herders

bicicleur
07-06-17, 09:37
Even their y is about 160,000 years old, which is extraordinary (A1b1b2). So, from that and other evidence we already knew that the ancestors of the Khoi population and all other populations on earth split 160,000 years ago, so this is effectively "just" pushing it back about 100,000 years. I haven't looked at all the calculations so I don't know if that's accurate, but 160,000 years is plenty long enough for a wow factor already. :)


Ted Kendall explains the 100.000 years difference :

https://www.facebook.com/groups/yfull/permalink/441150939581417/

https://www.nature.com/article-assets/npg/nrg/journal/v15/n5/images/nrg3707-f3.jpg

A very striking case is the immune system allele HLA-B*73.
This particular immune system allele (non-recombining segment) actually sits within a *chimpanzee* clade. It's rather rare among humans today, and interestingly, is found in various places in Southwest Eurasia and Europe (including 2% of Italians), but it was *not* found in Neanderthals and Denisovans. Immune system alleles are critical in fighting off disease, and having a variety of immune system alleles in a population ensures that if a certain set are uniquely susceptible to a deadly epidemic, other will always be around which can have an advantage. Also, people who are heterozygous will have an advantage over people who are homozygous in these situations. This is called "balancing selection". Obviously, this "chimpanzee" HLA-B*73 had some sort of advantage for ensuring the survival of those who carried it in certain situations, or it wouldn't have survived until today.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5203853/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677943/
HLA-B*73 allele frequencies:
https://en.wikipedia.org/wiki/HLA-B73
We can say then that the tMRCA of HLA-B*73 with the other HLA-B alleles predates the time of the human-chimpanzee split. (This is estimated to be 7-10 million years ago, with possible further admixture events at 6.3 and 5.4 million years ago). In this case, this allele will make some humans appear "closer" to chimpanzees than many others. However, that doesn't make 2% of Italians "chimpanzees". This is just normal "messy" speciation, that happens when the effective population size of the founders of a species is thousands of individuals.

MarkoZ
07-06-17, 14:26
Amazing. Has the split happened before Homo Sapiens Sapiens came to existence? Archaic San people might need new classification. ;)

A less racist interpretation would be that common archaeological reference points are greatly underestimated and mutation rates overestimated. It's what happens when the most important places in the prehistory of humanity are understudied compared to the West Eurasian sink.

I1a3_Young
07-06-17, 15:35
I wonder if the very few "A" found in early Europeans were similar to the San or not?

I need an afro-pedia!

Angela
07-06-17, 15:50
Here is a very helpful analysis from Razib Khan. He's indeed correct that blogger Dienekes foresaw a lot of this as much as 10 years ago. Yes, I've been following this topic for that long. :)

https://gnxp.nofe.me/2017/06/06/a-reticulation-pulse-expansion-of-modern-human-genetic-variation/

berun
07-06-17, 18:07
Principal 95 Component Analysis (PCA) and admixture analyses show that the three Stone Age individuals are 96 related to present-day Khoe-San groups, specifically to southern Khoe-San, such as the Karretjie People8 97 and the Lake Chrissie San23 (Figs. 1B-C, Extended Data Figs. 1, 7, 8, Figs. S6.1-S6.5, S9.6-S9.9). The 98 four Iron Age individuals all group with populations of West African origin/descent, specifically with 99 southeast Bantu speakers from South Africa (Figs. 1B-C, S6.1-S6.6). This observation is consistent with 100 archaeological evidence for the arrival of migrant Iron Age farmers of West African descent to the 101 eastern parts of southern Africa at ~1.7 kya24.

Just fine, genetics are going parallel with historic facts: the indigenous HG Khoisan of Y-DNA A1 are related autosomaly and by Y-DNA to the Stone Age individuals buried two millennia ago. The Iron Age individuals instead mate with the actual South African Bantus herders, whom colonized the area from Kenya 1500 years ago with their Y-DNA E. Even a Iron Age individual had a Khoisan / HG mtDNA, displaying so admixture with the colonists (which it's quite visible after looking at Mandela's face).


We tested various admixture-scenarios25 into Khoe-San groups using the good-coverage, high 109 quality, genome of Ballito Bay A (SI 6.4-6.5) and conclude that the admixture source was an (already 110 admixed) Eurasian/East African group (Extended Data Fig. 2, Extended Data Table 1 and 2), comparable 111 to the Amhara, today living in Ethiopia (SI Section 6.4-6.5). We estimate that Ju|’hoansi individuals 112 received 9-14% (Extended Data Fig. 2, Extended Data Table 2, SI 6.4-6.5) admixture from this mixed 113 East African/Eurasian group (69%/31%, Extended Data Fig. 2, and SI Section 6.5), and all Khoe-San 114 groups show 9-22% of this admixture (Fig. 2, Extended Data Table 2, SI 6.4-6.5). We dated this admixture event into the Khoe-San using admixture LD decay patterns25 to between 50 117 (±3) generations ago for the Ju|’hoansi (San) and 44 (±4) generations for the Nama (Khoekhoe) 118 corresponding to 1.5-1.3 kya (assuming 30 years/generation) (SI 6.6). The East African/Eurasian source 119 of the admixture is particularly pronounced in herding Khoe groups such as the Nama (Extended Data 120 Table 2, SI 6.4-6.5). Based on these results, we suggest a migration from East Africa into southern 121 Africa, resulting in admixture with local hunter-gatherers ≥1.5 kya.

Now it seems that logics are not working more: Bantus arrived some 1500 years ago but the people that admixed with the indogenous Khoisan were instead Amhara-like... OK, it is not so unusual shared migrations (Turks and Magyars to Hungary, Slavs and Avars to Hungary, etc.)... but the paper is not following a basic methodology: to take into account the history of the analysed population.

If they would have read "Strong Maternal Khoisan Contribution to the South African Coloured Population: A Case of Gender-Biased Admixture", which is not cited in the paper, they would know that Khoisans have mingled in the last centuries with local Bantus and European and Asian migrants.


It is remarkable that fully 60% of South African Coloureds mtDNAs belong to Hg L0d. This Hg, together with L0k, has been shown to be specific to the Khoisan peoples of South Africa (e.g., Juj’hoansi San, !Xun/Khwe, !Xun, and !Kung), and not to all click speakers; it is virtually absent from other populations across Africa.


The additional 19% of African maternal lineages observed in SAC comprise the various L0a, L1, L2, L3, L4, and L5 clades (Table 1), which are thought to have been introduced to South Africa during the recent Bantu expansion. 31,35 Because today these lineages are also observed in
the Khoisan (~40%),29,33,34 they should be seen as lineages of ‘‘pan-African’’ origin. Their presence among SAC reflects either direct gene flow from Bantu peoples or indirect Bantu contribution via admixture with the Khoisan, who have received these lineages through their prior admixture with Bantus.29 In the latter case, the actual maternal contribution of the Khoisan to the SAC population would be up to 79%.

The remaining of the mtDNA in SA Coloureds is 16% Asian and 4% European.


This component was clearly dominated by the pan-African Hg E-M2, which constituted 24.1% of the entire variation.
Hg E-M2 is restricted to sub-Saharan African populations; it reaches the highest frequencies (up to 90%) across Bantuspeaking
groups48 and varies in its distribution among Khoisan groups (~40%).33,34,49 Because the multiple Hg E-M2-derived branches do not exhibit a clear population clustering50 and microsatellite networks for paragroup E-M2 are noninformative as a result of the multiple reticulations observed (50 and data not shown), the presence of Hg E-M2 among the SAC, although it could attest to Khoisan contribution, can only be attributed to a
component originating south of the Sahara desert. Likewise, the presence of the Hgs E-M35 (xM78, M81, M123, M281) (3.5%) and B-M112 (1.3%), which are shared between Khoisan and Bantu speakers,33,34 reflect a general pan-African component. Actually, this phylogenetically unresolved pan-African component prevents the ability to test for a prior Bantu-to-Khoisan paternal gene flow, as demonstrated for the maternal side.


Finally, and in strong contrast with mtDNA results, only a minor fraction (5.3%) of the African paternal variation can be firmly attributed to the Khoisan, as attested by the presence of Hg A-M51, which has been observed only among Khoisan-speaking populations from Namibia and South Africa


Unlike the negligible European maternal component (<5%), the paternal contribution of West Eurasian lineages 51–53 to the SAC turned out to be very important (>32.5%) (Figure 1, Table 2). This is attested by the presence of Hgs R-M343 (18%), I-M170 (8.8%), R-M17 (5.3%), E-M78 (2.2%), T-M70 (1.7%), G-M201 (0.9%), and J-M304 (0.9%).


The least dominant paternal component observed in the SAC was that originating from south Asia56,58–61
(17.5%, Figure 1 and Table 2). F-M89 (xM201, M69, M170, M304, M9) (6.1%), H-M69 (2.2), and R-M124 (1.3%) are
primarily associated with Indian populations,58,62 andO-M122 (3.5%), O-M119 (1.7%), K-M9 (x M20, M186,
LLY22 g, M175, M45, M70) (1.3%) and O-M95 (0.9%) are mainly found in southeast Asian populations, including
China.59,61 The STR haplotype profiles associated with each of these Hgs were clearly consistent with Indian and
southeast Asian geographic origins, respectively. Similar to the maternal component, the paternal southeast Asian
lineages could have been introduced into the SAC population from Madagascar, via their prior existence among
Malagasy.42

The case is similar for Pygmy HG, the Bantu Y-DNA of their farmer neighbours is quite common among them, but no Bantu mtDNA is seen; the contrary happens among the Bantu neighbours: they have a good chunk of Pygmy mtDNA but few Pygmy Y-DNA.

So, if there was so much extensive admixture between Khoisan, local Bantus and migrants, it's possible to think that the inverse case was also usual??

Just looking at Genetiker tables, the Bushman South Africa, 5 have 100% black component, and 8 have 75% black component + 25% diverse components in different percents (WHG, EEF, Yoruba, Natufian...) which quickly demonstrates a recent admixture with diverse groups that is not yet leveled in such population.

This is the level of the last ancient DNA papers, it's a recent science and I understand it could not be firmly developed, but a few grams of logics and methodology is not harmful.

For the datation of the first humans about 260000... it's another aspect of the paper that I have no way to critizice by lack of enough spirit.

MarkoZ
07-06-17, 19:17
I wonder if the very few "A" found in early Europeans were similar to the San or not?

I need an afro-pedia!

Which are those HG A Europeans again?

Megalophias
07-06-17, 20:17
... but the paper is not following a basic methodology: to take into account the history of the analysed population.... If they would have read "Strong Maternal Khoisan Contribution to the South African Coloured Population: A Case of Gender-Biased Admixture", which is not cited in the paper, they would know that Khoisans have mingled in the last centuries with local Bantus and European and Asian migrants.

I hardly think it's likely they were unaware of that. What are you suggesting is the problem here?

berun
07-06-17, 22:25
I think this is the Amhara-like population that mixed with Khoi-Khoi / Namas:

https://en.wikipedia.org/wiki/Oorlam_people

the Euroasiatic East African population that admixed with the Khoisan came from...... Cape Colony... and admixed some two centuries ago. Fantastic fiasco!

It's so difficult that gene labs would contact historians ?

Megalophias
07-06-17, 22:58
Recent Dutch admixture does not sound like a plausible thing to be mistaken for >1000 year old East African admixture. Plus you'd need some kind of unlikely Bantu founder effect to account for all the E-M293.

And c'mon, the authors aren't total newbs.

berun
07-06-17, 23:36
You might read the link before saying Dutchs: newbs can do what you did now.

By the way:


According to them, there was intermarriage with the Sotho and other Bantu-speaking (non-Swazi) people long before they migrated to Lake Chrissie. It is also noteworthy that some Swazi groups such as the amaNgqamane historically raided the Lake Chrissie area in search of booty (Prins 1999). This included the children of neighboring tribes including San individuals who were abducted to become serfs known as the titfunjwa. These captives formed an important part of the Swazi economy and were assimilated into Swazi society (ibid). Although Swazi men often took San concubines, children of these unions frequently escaped and reunited with independent San groups (F. Prins fieldnotes 1998). By these processes, there was gene flow in both directions.


The existing genetic composition, of the increasingly admixed San, could have been further affected by non-African populations who arrived and traded along the east coast of Africa. The 16th and 17th centuries saw various Portuguese shipwrecks along the coastline of the current KwaZulu-Natal and the Eastern Cape provinces. Many of the survivors of these shipwrecks were lascars (i.e., Muslim slaves of Indian origin) (Crampton 2004). According to Duma elders, some of these people of Indian origin did not follow their Portuguese masters back to Europe. Rather, they opted to stay on the southeastern coast of Africa, where they eventually intermarried with local inhabitants. It appears that San admixture at the coast intensified even more during this period, and Duma informants maintain that some Indian people intermarried with the local San, assimilating with them. Around the middle of the 18th century, the Mpondomise people left the coastal areas of the current Eastern Cape, and settled for a while along the middle reaches of the Mzimvubu River, eventually establishing themselves in the foothills of the Eastern Cape Section of the Drakensberg near Elliot (Derricourt 1974). It appears that they may have been accompanied by their San relatives and friends, who at this stage would have experienced marked acculturation. ...Nevertheless, the Indian ancestral contribution to the present Duma San is widely acknowledged. Locally, some of the Duma San are called the Sulumani. Duma informants are quick to point out their distinct long hair, aquiline features, and the fact that they still practice a form of Kosher (Albert Duma pers com 2011) (F Prins fieldnotes 2009-11).


Apart from the Duma San of possible Indian descent (i.e., the Sulumani), they further self-identify as those of European or Coloured descent (i.e., amaColoured Duma), and those closest to their original San forebears called (Abathwa Duma). Informants maintain that early European or Coloured traders and adventurers often intermarried with their forebears, a fact also supported by historical documentation relating to Mountain San relationships with other groups in the greater ‘No man’s Land’ region during the 19th century (Challis 2008).


’Karretjie’ is the Afrikaans word for a small vehicle, alluding to a mobile lifestyle based on the use of donkey carts. Throughout the great Karoo region of South Africa, there are small bands of people living this mobile lifestyle, but due to recent socio-economic changes, this lifeway is quickly disappearing. The Karretjie People phenotypically resemble Khoe-San people. Oral and archaeological records also suggest Khoe-San ancestry, but the group completely lost their original linguistic and socio-cultural affinities. They sometimes self-identify as Coloured and speak Afrikaans. Genetic studies indicate a predominant San ancestry for the Karretjie People, with small amounts of Bantu-speaker and European admixture (coming mostly from the male side, following Y-chromosome studies) (Schlebusch et al. 2011; Schlebusch et al. 2012). The San ancestry is a southern San component – related to, e.g., the ǂKhomani. East African admixture is minimal (compared to the substantial component of East African ancestry in the KhoeKhoe group – e.g., the Nama (Breton et al. 2014; Schlebusch et al. 2012)), and therefore the ancestry of the Karretjie People is inferred to be mostly from southern San, rather than from Khoekhoe ancestors. The southern San groups living in these regions until the late 1800s were speakers of the sout hern San |Xam language .... Males that were not killed by hunters fled into the hilltops or were sent off to prison. Females and children were relocated to farms where they served as farmhands, the (aka tame Bushmen) (De Jongh 2002, 2004). Khoekhoe herders living in the area were also in competition with colonists for grazing land, but they claimed right to certain areas and owned cattle to trade with the Europeans.. ... The descendants of some of the relocated |Xam females and children still live on European owned Karoo farms where they became admixed with the local Xhosa population (Bantu-speaking farmers). Amongst the older generation of European farmers, there are still a few who recognize the presence of labourers with San decent. Such persons were known to possess wanderlust, and refused to settle in one place. These people became the Karretjie People, with their donkey carts as mobile units, perpetually on the move to do different periodic jobs (De Jongh 2002, 2004).

berun
07-06-17, 23:37
In whichever case an admixture anlisys that is not taking into account such recent admixtures is useless.

berun
08-06-17, 00:10
Just try to sample 100 Londoners randomly, forget any recent migration there, and try to do some admixture analysis as to know the history of England. I guess that the lab would be capable to find out an admixture event 1500 years ago with a Yemen-like pop.
:)

Megalophias
08-06-17, 01:20
I don't actually think you could get 100 Londoners to come out as a 1500 year old single-admixture with Yemeni LD curve, that's a trick I'd like to see. :grin:

The Ju|hoan in ADMIXTURE came out without a Eurasian admixture component, where some of the other Khoisan did show such components. They have a single, old admixture LD signal, while Nama show two West Eurasian admixture signals, one recent.

Barbieri's pooled Khoisan sample (n=371) has 15% E-M293 and 3% CF. Tishkoff's pooled !Kung sample (n=103) has 11% E-M35 and 0% CF.

There's just no evidence that they have substantial recent Eurasian ancestry, and lots of evidence that they have substantial ancient East African ancestry.

LeBrok
08-06-17, 02:48
A less racist interpretation would be that common archaeological reference points are greatly underestimated and mutation rates overestimated. It's what happens when the most important places in the prehistory of humanity are understudied compared to the West Eurasian sink.
I thought that my joke was obvious, did you miss the blink at the end? You should know me better by now.

berun
08-06-17, 09:03
I can't accept admixture analysis with recently mixed population, that is a basic rule (and much less to accept dating our spice with them!).


The Oorlams Edit
In the 19th century white farmers, mostly Boers, moved farther north, pushing the indigenous Khoisan peoples, who put up a fierce resistance, across the Orange River. Known as Oorlams, these Khoisan adopted Boer customs and spoke a language similar to Afrikaans.[2] Armed with guns, the Oorlams caused instability as more and more came to settle in Namaqualand and eventually conflict arose between them and the Nama. Under the leadership of Jonker Afrikaner, the Oorlams used their superior weapons to take control of the best grazing land. In the 1830s Jonker Afrikaner concluded an agreement with the Nama chief Oaseb whereby the Oorlams would protect the central grasslands of Namibia from the Herero who were then pushing south. In return Jonker Afrikaner was recognised as overlord, received tribute from the Nama, and settled at what today is Windhoek, on the borders of Herero territory. The Afrikaners soon came in conflict with the Herero who entered Damaraland from the south at about the same time as the Afrikaner started to expand farther north from Namaqualand. Both the Herero and the Afrikaner wanted to use the grasslands of Damaraland for their herds. This resulted in warfare between the Herero and the Oorlams as well as between the two of them and the Damara, who were the original inhabitants of the area. The Damara were displaced by the fighting and many were killed.

The it will be good to read a bloody page of the history about them:

https://en.m.wikipedia.org/wiki/Herero_and_Namaqua_genocide

shake well and thereafter get dates of old admixtures and even date the human race, even dancing over a dead cat would not make me more happy...

berun
08-06-17, 21:28
OK Megalophias, the authors are aware of recent admixture:


All modern-day Khoe-San are drawn towards other 105 Africans and non-Africans compared to the ancient individuals from Ballito Bay, including Ju|’hoansi 106 San, thus far thought to be the least affected by recent admixture8, 9.


The 123 migration had a pronounced impact on all current Khoe-San groups, not only on the descendants of Stone 124 Age herders, such as the Khoekhoe (Fig. 2B, Extended Data Table 2, SI 6.4-6.5). This has been an elusive 125 result since all modern-day Khoe-San individuals display ≥9% recent admixture.

But the reference of Pickrell / Barbieri in "The genetic prehistory of southern Africa" is providing correct arguments for known migrations:


The positions of the Nama individuals in Supplementary Figure S2 are suggestive of post-colonial European admixture, in accordance with historic documentation of European ancestry in some Nama groups [23] . To test this, we used four-population tests [26] of the form [[Yoruba, X],[Han, French]], where X is any southern African population. A positive f4 statistic indicates gene ow between X and a population related to the French (or alternatively gene ow between populations related to the Yoruba and Han). The most strongly positive f4 statistic in the southern African populations is for the Nama (Supplementary Figure S6A), as expected if they have experienced European admixture. To conrm the direction of this gene ow, we used ROLLOFF [27] to test if there is detectable admixture LD in the Nama. If we use the Juj'hoan North and the French as the putative mixing populations, there is clear admixture LD (Supplementary Figure S6B), we date this mixture to approximately ve generations (150 years) ago.

They identify correctly a recent European ancestry (displayed in Figure S8 quite clearly: the Nama have around a 20% of Basque / French orange admixture), leaving so the Bantu ancestry as old...


These dates are consistent with archeological evidence for the arrival of both East African pastoralists and agriculturalists (probably Bantu speakers) in southern Africa 2,000–1,200 years ago32–35. PCA suggests that the majority of admixture in the Khoisan is more closely related to the Yoruba (from West Africa, linguistically related to Bantu speakers) than to the Dinka (from northeastern Africa; Supplementary Fig. S5), although our data are consistent with additional East African ancestry in some Khoe speakers (Supplementary Methods).

Instead, the recent paper is providing an old Eurasian/African phantom migration.

holderlin
09-06-17, 16:49
hot damn. missed this one. Coinciding with the discovery of what initially appears to be AMH in North Africa 300k ya.

The picture will continue to get more interesting.

It continues to amaze me that every era of science thinks that "everything has been discovered".

Megalophias
09-06-17, 18:52
OK Megalophias, the authors are aware of recent admixture....
Of course they are aware of recent admixture, for heaven's sake.

I have no idea why you think that cryptic colonial admixture that inexplicably appears many times older than it is and leaves no uniparental signature is a better explanation than old East African admixture that leaves the proper LD curve, an East African Y haplogroup, and East African lactase persistence alleles.

berun
09-06-17, 21:23
They are aware of recent admixture... but they don't deal with it. In fact is just the contrary as *****ell-Barbieri paper as they blend recent European and old Bantu admixture as to get an Afroeurasian old admixture. For lactase persistence it is just was received from the first Bantu colonists, and it's shared with the Xhosa. For such east African haplo it's not shared by Bantu neighbours, right?

Megalophias
09-06-17, 22:09
They are aware of recent admixture... but they don't deal with it. In fact is just the contrary as *****ell-Barbieri paper as they blend recent European and old Bantu admixture as to get an Afroeurasian old admixture. For lactase persistence it is just was received from the first Bantu colonists, and it's shared with the Xhosa. For such east African haplo it's not shared by Bantu neighbours, right?

There are plenty of papers on this subject. I find the East African scenario much more convincing than a magic hybrid Bantu + colonial Eurasian scenario. I'm heading out of town now, so you can have the last word.

Angela
13-06-17, 16:50
A review of these recent papers by Razib Khan: The search for Eden
https://gnxp.nofe.me/2017/06/11/the-search-for-eden-opens-up-new-vistas/?utm_source=dlvr.it&utm_medium=twitter

berun
13-06-17, 19:15
There are plenty of papers on this subject. I find the East African scenario much more convincing than a magic hybrid Bantu + colonial Eurasian scenario. I'm heading out of town now, so you can have the last word.

Do you take quantity as quality?

In whichever case even in the Khoisan tribes with less East African Eurasian admixture the genetists have found genetic "outliers", and that is like to say migrants... but everybody is free to believe in ghosts, or ghost pops.

berun
15-06-17, 21:33
One of the many papers is that one written also by our beloved D. Reich "Ancient west Eurasian ancestry in southern and eastern Africa":


We began with an analysis of population mixture in southern Africa, using the data from Pickrell et al. (3) supplemented with
an additional 32 individuals from seven Khoisan populations genotyped on the Affymetrix Human Origins Array (SI Appendix,
Table S1); note that the Damara are excluded from most of the subsequent analyses because they genetically resemble southern
African Bantu-speaking groups (3). These southern African data were then combined with previously published worldwide
data (5) (SI Appendix). After removing individuals who seemed to be genetic outliers with respect to others in their population
(SI Appendix),

It's quite obvious the tricks here.


We thus computed weighted LD curves in the Juj’hoan_North, using the Juj’hoan_North themselves as one reference population and a range of 74 worldwide populations as the other, and examined the amplitudes of these curves (Fig. 1A). The largest amplitudes are obtained with European populations as references (Fig. 1A); taken literally, this would seem to implicate Europe as the source of admixture (although Middle Eastern populations are also among the best proxies). The estimated date for this gene flow is 43 ± 2 generations [1,290 ± 60 y, assuming 30 y per generation (7)] before the present, consistent with our previously estimated date (3). This date is well before the historical arrival of European colonists to the region.

big LOL!!


Under a model of admixture from a single source population, the decay rate of the LD curve does not depend on the
reference population used (6); this suggests that there are at least two separate non-Khoisan sources of ancestry in some of these
Khoisan populations.

yes! they have found two admixture events, maybe old Bantu and recent Coloured? let's see them...


The two inferred mean admixture times in the Gkana are 4 ± 1 and 39 ± 6 generations ago. ... By examining these amplitudes,
we conclude that the west Eurasian ancestry in the Gkana entered the population through the older admixture event (Fig. 3). Because of the caveat noted above, however, we cannot distinguish between two historical scenarios with this method: direct gene flow from a west Eurasian population and gene flow from a west Eurasian-admixed population.

superb!


The Taa_West also show two episodes of west Eurasian admixture, but the more recent one has low confidence. ... this method fails to detect that the Naro are admixed between two distinct Khoisan groups (3), and we find evidence of west African ancestry in just four Khoisan populations (!Xuun, Gkana, Khwe, and Taa_East) when treated individually (but see analyses of combined populations below).

a method also could fail if data is badly entered and interpreted:


in contrast, there is considerable genetic drift in west Eurasian populations because of the out-of-Africa bottleneck, which allows
admixture events to be more confidently assigned to this ancestry ... To increase our power to detect additional admixture
events, we performed analyses of combined populations. In a combined set of populations (the Tshwa, Shua, Haikom,
ǂHoan, Naro, and Taa_North) that have marginal evidence for a second, more recent admixture event, we infer two dates of
admixture: one 40 ± 2 generations ago and one 4 ± 1 generations ago (Z-score for the hypothesis that the admixture time is zero is
3.2, P = 7 × 10−4). In a combined set of two populations (the Juj’hoan_North and Gjui) that have marginal evidence for
a second, more ancient admixture event, we also infer two dates of admixture (SI Appendix, Fig. S24), but with different dates
from all other samples: one 30 ± 4 generations ago (Z-score of 6.9, P = 2 × 10−12) and one 109 ± 41 generations ago (Z-score of
2.6, P = 0:005). We interpret this as suggestive evidence that the population that introduced west Eurasian ancestry to southern
Africa was itself admixed, and that this more ancient admixture happened around 110 generations ago (although the confidence
intervals here are clearly large). ... The highest levels of west Eurasian ancestry are found in Khoe–Kwadi speakers (Table 1, southern Africa), particularly the Nama, where our estimate of west Eurasian ancestry reaches 14% (although note we cannot distinguish between the impact of recent colonialism and older west Eurasian ancestry in the Nama using this method).


∼1% of this is west Eurasian ancestry (Table 1) and the Juj’hoan_North have no Bantu-related ancestry, then this gives an admixture proportion of ∼25% west Eurasian ancestry in the putative eastern African source population. Using this value, we then estimated the proportions of Khoisan, putative eastern African, and Bantu-related ancestry of all populations using a linear model (18)

ops! another trick!

The table 8 of the supp is just telling what fiasco was done: the samples Bantu tribes have some 7-30% of Khoisan ancestry... but 0% of Eastern Africa/Eurasian ancestry... how in the hell it's possible that the Eurasian genes would be skipt when Bantus and Khoisans admixed in the huts? they had near the bed a DNA lab much more sophisticated than that of Reich?

By the way the paper is conscious about recent Eurasian admixture in the Nama, but is not saying nothing about genocide, rapes and camps in Namibia, or the existence of Coloureds.

berun
17-06-17, 07:42
Also a pitfall to believe in a ghost migration of mixed East African / Eurasian population is the fact that Khoisans have 0% of haplo J, as it's shared by some 70% of Arabian Arabs and a 33% of Amhara (clealy the responsible to deliver the Semitic languages in Ethiopia). If the ghost migration was 25% Eurasian why Khoisans have no such haplo?

By the way some maps are quite expressive:

8864

8865

the presence of Afrikaans is debt to Oorlams and Basters from South-Africa, already mixed pops. In SA itself Afrikaans is the mother language of 60% of the whites, 76% of the Coloureds, 600000 Negroes and 60000 Asians.

8866

this map reminds somehow the American "Indian Reservations"...

berun
30-06-17, 19:06
This is from "Fine-scale human population structure in southern Africa reflects ecological boundaries":


This South / East Asian ancestry is not confined to the SAC [Couloured] population, as attested by the presence of the M36 mitochondrial haplogroup. The M36 mitochondrial haplogroup (South Indian/Dravidian in origin) is present in two out of 64 ≠Khomani San matrilineages,
(Table 1). The presence of M36 is likely derived from slaves of South Asian origin who escaped from Cape Town or the surrounding farms and dispersed into the northwestern region of South Africa. In addition, we observe one M7c3c lineage in the Nama (Table 1), which traces back to southeastern Asia but has been implicated in the Austronesian expansion of Polynesian speakers into Oceania (Kayser 2010; Delfin et al. 2012) and Madagascar (Poetsch et al. 2013). The importation of Malagasy slaves to Cape Town may best explain the observation of M7c3c in the Nama.

you can sum up the mutations of Indians, Austronesians, Khoesans, Dutchs, Xhosa, etc. and thereafter you get that the Homo sapiens is old as the dinosaurs... well, after looking how seem to dismiss data some genetists I will go to write down a paper like "Recent Corvus corax admixture in Europeans" as to be readily published in some respectful review as Nature or any yellow paper alike (they will sell more with such enthusiastic and awesome discoveries), and thereafter I will get more grants for my lab (institutions will verify that I publish in important pamphlets so I will be taken as a serious researcher). Red alarm: science had holy cows but now it has also charlatans.

berun
11-07-17, 15:33
In Wood (2005) the Herero have a 8% I Y-DNA and 14% R..................................... I go to write down a paper about Homo sapiens dating about 1500000 years ago, and that the major diversity in Namibia of unrelated branches or more regional divergence provides evidence that Europeans are mainly pale Africans of recent arrival. Please deliver the grants to Bank of Bantustan before Reich or somelse would steal the idea.