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Author Topic: Ancient Tanzanian Pastoralist results... VERY interesting stuff!
Askia_The_Great
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But first shout outs to Djehuti. You were right on the money.

Anyways...
http://www.cell.com/cell/fulltext/S0092-86741731008-5

Many on the site Forumbiodiversity were certain this pastoralist would be more "Cushite-Like" with lineages like E-V22/M1 instead we get what I call "true Bantu Negroid" L2a1.

Here is the summary-
quote:
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.
Thoughts?
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Elmaestro
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Ayo Capra where you at man! lmao
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Punos_Rey
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Also found these tidbits interesting

"Western-Eurasian-related ancestry is pervasive in eastern Africa today (Pagani et al., 2012, Tishkoff et al., 2009), and the timing of this admixture has been estimated to be ∼3,000 BP on average (Pickrell et al., 2014). We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia. These results could be explained by migration into Africa from descendants of pre-pottery Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East." PR: Basal Eurasian?

"While these findings show that a Levant-Neolithic-related population made a critical contribution to the ancestry of present-day eastern Africans (Lazaridis et al., 2016), present-day Cushitic speakers such as the Somali cannot be fit simply as having Tanzania_Luxmanda_3100BP ancestry. The best fitting model for the Somali includes Tanzania_Luxmanda_3100BP ancestry, Dinka-related ancestry, and 16% ± 3% Iranian-Neolithic-related ancestry (p = 0.015). This suggests that ancestry related to the Iranian Neolithic appeared in eastern Africa after earlier gene flow related to Levant Neolithic populations, a scenario that is made more plausible by the genetic evidence of admixture of Iranian-Neolithic-related ancestry throughout the Levant by the time of the Bronze Age (Lazaridis et al., 2016) and in ancient Egypt by the Iron Age (Schuenemann et al., 2017)."

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Elmaestro
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Thinks to look at...

-Luxmada, the Tanzanian pastoralist clusters with Nilotic populations however is best modeled by Mota + PPNB(37%). This Near Eastern component is hardly EEF and lacks minor Iranian Admixture as do modern Cushitic populations. The high proportion of Near-east related Ancestry in respects to Luxmadas clustering position is anomalous... unless you attribute the Near eastern signatures to an indigenous African population structure ofcourse. ...see Ifri n'Amr or Moussa (IAM) Fregel et al 2017.

-Modern west African could have sustained an episode or two of drift which in combination with heterogeniety due to recombination with Ancient African populations pulls them away from the other African populations before the bantu expansion. This may be evident in the Eurasian "signals" widespread in Malawi and south Africa before the bantu expansion.

-The Hadza retains an Ancient East African component peripheral to Mota... Not really elaborated here but there's signs that they're Ancient genetic influence might extend beyond the continent to the East.

-The 2.6kya Pemba Agriculturalist is straight outa West Africa, I'm concerned about previous hypothesis about a secondary expansion from Malawi.

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beyoku
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quote:
Originally posted by Elmaestro:

-Luxmada, the Tanzanian pastoralist clusters with Nilotic populations however is best modeled by Mota + PPNB(37%). This Near Eastern component is hardly EEF and lacks minor Iranian Admixture as do modern Cushitic populations. The high proportion of Near-east related Ancestry in respects to Luxmadas clustering position is anomalous... unless you attribute the Near eastern signatures to an indigenous African population structure ofcourse. ...see Ifri n'Amr or Moussa (IAM) Fregel et al 2017.
.

Fvcked At both ends....
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Askia_The_Great
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@Capra

Your thoughts?

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xyyman
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I did not write this….honest. He! HE! HE!
1. San Peoples probably occupied all of Africa maybe into Europe
2. Modern West Africans are probably new to West Africa
3. Modern West African carry very archaic admixture(Dienekes and I).
4. Europeans are a sub-set of Africans


Quote
SUMMARY
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent
lineage that comprises the primary ancestry of the southern African San had a wider distribution in
the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers 8,100–

2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers 1,400
years ago. We document how the spread of farmers from western Africa involved complete replacement
of local hunter-gatherers in some regions, and we track the spread of herders by showing that the
population of a 3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern
to southern Africa,
including a 1,200-year old southern African pastoralist. The deepest diversifications
of African lineages were complex, involving either repeated gene flow among geographically
disparate groups or a lineage MORE deeply diverging than that of the San contributing more to some western
African
populations than to others. We finally leverage ancient genomes to document episodes of
natural selection in southern African populations.

INTRODUCTION
Africa harbors more genetic diversity than any other part of the world (Cann et al., 1987; Tishkoff et al., 2009). This is reflected
both in a higher average number of differences among sub- Saharan African genomes than among non-African genomes
(Cann et al., 1987; Ramachandran et al., 2005) and in the fact that the ancestry found outside of Africa is largely a subset of
that within it
(Tishkoff et al., 2009). Today, some of the earliest branching African lineages are present only in populations with
relatively small census sizes, including the southern African Khoe-San (see STAR Methods for terminology), central African
rainforest hunter-gatherers, and Hadza of Tanzania (Gronau et al., 2011; Schlebusch et al., 2012; Veeramah et al., 2012).

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Without data you are just another person with an opinion - Deming

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xyyman
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See ELMaestro. That is the problem with you white people. "Forest for the trees". You go in with pre-conceived notions without looking at the data. Like that new paper on ancient North Africans you people are quoting.

The data shows that North Africans and Levantines and at least southern Europeans were black skinned up to 4000bc. Carrying African ancestral forms of pigmentation. Now this paper prove I am right about Africa. I should be paid for this shyte. lol!


The problem is you people can't read the data and analyze it. You rely on lying Europeans to put their spin on it. Europeans have been historical liars. That is why I am on to their spin and lies.

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Without data you are just another person with an opinion - Deming

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capra
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Had to work last night so not done reading it yet.

Malawian foragers look like their own thing. Not sure it's totally extinct ancestry, they have a bunch of L0k2, which has previously been identified as a haplgroup Southern Bantu acquired to the northeast of their current location.

Seems like fairly pure Hadza or Mota like people were all over East Africa until quite recently (although that is probably lumping together a lot of quite different populations). 1400 years ago on Zanzibar okay, but someone 400 years ago on the coast of Kenya apparently had no Bantu ancestry, would not expect that. (Related to Dahalo maybe? They have that click substrate.)

South_Africa_1200BP is like a Nama without Bantu or extra European ancestry, which makes sense - an ancestral Khoe pastoralist. Modelled as around half (or more) Tanzanian Pastoralist - at least twice as much as you'd expect from the last paper, which used Amhara as a reference. TP is probably not a perfect reference either of course. But this level of admixture would definitely favour the Khoe language family arriving from East Africa as some linguists have suggested (it may be related to Sandawe).

Not sure what's anomalous about how the TP clusters?

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xyyman
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Here is more spin and BS…First the 3100BP Tanzanian carried as much as ****40%***** Levantine (not Iranian or Turk) AIM. So what do they do? They increase the age of Pre-Pottery in the Levant to 10,000years!!! Thus trying to visualize a very ancient origin in the Levant. But yet admit….talk about “Fake News”.

Liars had to admit the , yes, there is a possibility this Eurasians AIM found in ancient Tanzanians may be African after all


--

Anyone understand what they are saying on page 65 2nd paragraph? Reading through their spin. Are they saying that the 1200year old South African already had “west Eurasian” ancestry. BEFORE modern colonial Europeans entered south Africa. When Pickerell et al published his paper I wondering where they were going with that, now I know. They already knew that “Eurasian” ancestry was indigenous to Africa. They were setting up the scenario to BS when more results came out. Guess what Eurasians are a subset of Afrcans. It existed in Africa BEFORE Eurasians existed.


Quote: “We found that the _3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna
Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-
year-old pre-pottery farmers of the Levant
(Lazaridis et al., 2016), and we can **exclude **source populations related to early
farmer populations in Iran and Anatolia. These results could be explained by migration into Africa from descendants of pre-pottery
Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_
3100BP descend from a common ancestral population that lived thousands of years earlier in Africa
or the Near East. We fit the
remaining approximately two-thirds of Tanzania_Luxmanda_ 3100BP as most closely related to the Ethiopia_4500BP
(p = 0.029) or, allowing for three-way mixture, also from a source closely related to the Dinka (p = 0.18; the Levantine-related
ancestry in this case was 39% ± 1%)
(Table S4).”

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Without data you are just another person with an opinion - Deming

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xyyman
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They are re-inventing multi-regionalism in Africa. This is a bomb shell. Anyone want me to explain this? Capra? ElMaestro, Cass, DJ, Beyoku, Sweetness, Sage? This is where the rubber hits the road.

Quote:” In particular, we find that ancient southern Africans, who have NONE of the eastern African admixture
that is ubiquitous today
, share significantly more alleles with present-day and ancient eastern Africans (including Dinka,
Hadza, and Ethiopia_4500BP) than they do with present-day western Africans (Figure 3B; Table S6). Even within present day
western Africans, the genetic differences between Yoruba from Nigeria and the Mende from Sierra Leone are inconsistent
with descent from a homogeneous ancestral population isolated from ancient southern Africans
. The asymmetry between
Yoruba and Mende is ALSO OBSERVED WITH NON-AFRICANS but is no stronger than in eastern Africans (the most closely related Africans
to the ancestral out-of-Africa population), and thus these signals are not driven by admixture from OUTSIDE Africa and
instead likely reflect demographic events entirely WITHIN Africa (Figure 3C; Table S6).”


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Without data you are just another person with an opinion - Deming

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capra
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have you forgotten all your wrong predictions already, xyyman? is it senility, or are you just pretending?
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xyyman
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Wow!! This is what I have been waiting for.
I said – there was never a Bantu Expansion. That modern west Africans are a misture of East African and another set of Africans that existed in West Africa. They are related to WHG. If they test Cape Verde they will carry the highest ancestry of this type of all West Africans. I said West Africans are primarily Neolithics

Quote:
“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
. Our genetic data do NOT support the theory that this putative basal lineage
diverged prior to the ancestors of Neanderthals, since the African populations we analyze here are approximately symmetrically
related to Neanderthals


--------------------
Without data you are just another person with an opinion - Deming

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xyyman
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You people and your delusion. Name one!? I have been bang on form the git go! Guess you did not read the paper. He! HE! HE! You don't have to. I am doing it now. re-read the above several times over. Ho!

quote:
Originally posted by capra:
have you forgotten all your wrong predictions already, xyyman? is it senility, or are you just pretending?

BTw- Anyone looked at Table 1. Notice no E1b1a. Also they used BT. Which includes ALL yDNA haplogroups except A & B. Do you want to know why? They have the results. Trust me! They want to let you Euronuts down first. Don’t want you jumping off the ledge. If I am a betting man. It is some earth shattering result like R1b-V88 or something like that. Come on Euronuts…calm down. He! HE! The best is yet to come.


Capra said: ".and yeah Xyyman, we're all waiting for you to catch up, I figure it'd take a while considering your obsession for tryna claim all those European lineages were GreatLakes somehow, then from there showing how horners are better proxies for AEgyptions... you know.... jumping from one wrong conclusion to the other.

And yes, Eurasian signatures in the Malawi etc. are not necessarily indicative of Eurasian admixture."


I said the Abusir are Africans like Tanzanians. Kenyans, Ugandans not necessarily Ethiopians ONLY. This is what the genetic data shows. we now see "Eurasian" Levant ancestry (not Turks) has been in Africa before there were "Eurasians".

--------------------
Without data you are just another person with an opinion - Deming

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Elmaestro
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@Capra

Well of course to YOU, this wouldn't be anomalous.. just speaking in general in terms of how people generally envision cushitic/horner involvement with prehistoric North Africa.

...and yeah Xyyman, we're all waiting for you to catch up, I figure it'd take a while considering your obsession for tryna claim all those European lineages were GreatLakes somehow, then from there showing how horners are better proxies for AEgyptions... you know.... jumping from one wrong conclusion to the other.

And yes, Eurasian signatures in the Malawi etc. are not necessarily indicative of Eurasian admixture.

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Askia_The_Great
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quote:
Originally posted by Elmaestro:


And yes, Eurasian signatures in the Malawi etc. are not necessarily indicative of Eurasian admixture.

Its most likely indirect if anything.
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xyyman
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Mod Warning-


I'm getting tired off you and derailing this thread. Knock it off...


[ 22. September 2017, 02:38 PM: Message edited by: Elite Diasporan ]

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Without data you are just another person with an opinion - Deming

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xyyman
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You are such a p....princess oops! prince

PR: Enough!

[ 22. September 2017, 08:45 PM: Message edited by: Punos_Rey ]

--------------------
Without data you are just another person with an opinion - Deming

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Clyde Winters
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This paper should not claim to be related to the entire prehistory of African people. The study only indicates that the San was the dominant group in much of Central, South and East Africa. This was obvious from a perusal of the location of the San in modern times.

The Niger-Congo speakers and Nilo-Saharans were predominantly North African and Sahel-Saharan people. As a result, you would not find these populations in Central and Southern Africa until after the fall of Egypt, as proven by the results of this study.

It was after the fall of Egypt that the Bantu spread into East-Central and Southern Africa. Other Sub-Saharan populations began to migrate out of Morocco, Mauritania and etc., into West Africa.

--------------------
C. A. Winters

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capra
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If you were a betting man, xyyman, you'd be living in a cardboard box. Table S4, the Malawian Y haplogroups are BT(xCT), so B or some extinct relative, not C, D, E, or F. It would be nice to know what kind exactly; B2b predominates in Mbuti and Hadza and is common in San and others, so would fit.

The Cape foragers have A1b1b2a, like the Ballito Bay men from the previous paper, quite far away. Wonder where the A1b1a1a and B2b were lurking.

What's Eurasian in the Malawians? A bit in ADMIXTURE at low K, but that doesn't mean much.

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capra
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OK, one of the two 6100-year-old foragers from Fingira in northern Malawi had B2b1a1a-M8357; the other had unresolved B2b1 (lower coverage), could be same clade or not.

The (probably) ~8100-year-old man from Hora 1, also in the north of Malawi, had pre-B2b1b1a-Y25096.

Both B2b1a and B2b1b lineages are common among Khoisan, Eastern and Western Pygmies, and some East Africans (plus Arabians). The major branches of these are old, at least 30-40 thousand years, and I don't know which if any modern people these Malawians would be closer to.

Archaeologically they were apparently belonged to Nachikufan II and related Late Stone Age cultures, characterized by various sorts of microliths, bored stones, ground stone axes, bone points and beads. Vague similarities to cultures further north and south but I have no idea how it might all be connected in the grand scheme, anyone know anything about this period?

Most of the middle belt of Africa may have been dominated by B2b from around 50 000 to 5000 years ago, with A1b1 pushed to the north and south of that, and upstream branches of A and B more to the northwest?

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Elmaestro
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@Doug please understand, Different researchers, different excavators, different publishers... they all want to get payed. So they'll leave space for future studies and split samples and teams so on and so forth...

@Capra I apologize, this thread was off to such a slow start, which was confusing to me because it is pretty huge imo... I personally believe they could have used a greater SSAn Dataset but ehh.

I would like to point out that with the exception of the maybe 400bc Kenyan and Luxamanda, North Africa is rather irrelevant for this dataset. Idek why folks are bringing up V88, for the love of me...

The most interesting thing here is the plethora of qpGraphs with multiple terminals and the story they tell.

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capra
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@Elmaestro

Yeah, they could have put in a lot more populations. But hey, leaves something for other groups to do I guess.

Finally got to the qpGraphs. OK, something that's bugging me - does it even make sense to say less admixture is more parsimonious because you have to posit admixture events? You could just as well say it's less parsimonious because you have to posit barriers to gene flow. Lack of admixture arrows every which way seems more of a necessary evil than a virtue.

I was wondering why they seem to be favouring the Basal African ghost over just Yoruba being closer to East Africans - but looking at those D stats everyone is closer to Yoruba than to Mende - even Mandenka. Crazy!

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Elmaestro
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quote:
Originally posted by capra:
@Elmaestro

Yeah, they could have put in a lot more populations. But hey, leaves something for other groups to do I guess.

Finally got to the qpGraphs. OK, something that's bugging me - does it even make sense to say less admixture is more parsimonious because you have to posit admixture events? You could just as well say it's less parsimonious because you have to posit barriers to gene flow. Lack of admixture arrows every which way seems more of a necessary evil than a virtue.

I was wondering why they seem to be favouring the Basal African ghost over just Yoruba being closer to East Africans - but looking at those D stats everyone is closer to Yoruba than to Mende - even Mandenka. Crazy!

I'm not entirely sure but it looks like what little differences in Basal African Ancestry between the Mende and YRI is what defines how close other populations are to either of them. Mende having more Basal African Ancestry siglehandedly makes all other African populations closer to the Yorubans. Mbuti being representative of an early split just became less significant, as maybe even THEIR ancestry is drifted away considerably from the "ghost" African Ancestor. Yorubans as well as maybe all Bantu populations might have more Mbuti-like/(RHG) Admixture than the Mende.

~Reffering back to Patin 2017, elevated levels of RHG seems synonymous with scoring higher for Mbuti in comparison to Mota, It looks like YRI have admixture from Mbuti, and Basal African, and maybe more... this series of recombination is probably what shapes the west African genetic landscape, and that small amount of Archaic African means a lot... There's nothing parsimonious about less Admixture events, it's just convenient if you ask me, I don't think it's intentionally misleading though. The new South African Hunter Gatherer genomes puts the Mota->West African relationship in check, they have to explain why such a Divergent lineage (SAHG) shows closeness (relative to West Africans) to Mota.

But also, there's another thing.... The root population is modeled off of Neanderthals and Denisovan, so we have to Account for that as well. We can probably put together a working general phylogeny of Early human history now, but seems very webbed.

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I'm REALLY going beyond losing my paitence. This thread is about the Tanzanian pastoralist... NOT North Africans, silly conspiracies or any other off topic nonsense. If you have an issue with this article then make your OWN thread.


Anymore derailment will be met with me contacting Punos Rey.

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Clyde Winters
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quote:
Originally posted by Elite Diasporan:
I'm REALLY going beyond losing my paitence. This thread is about the Tanzanian pastoralist... NOT North Africans, silly conspiracies or any other off topic nonsense. If you have an issue with this article then make your OWN thread.


Anymore derailment will be met with me contacting Punos Rey.

Clearly you have not read your own article. It is the authors themselves who bring up North Africa and the Middle East. Punos_Rey was the first writer to note the authors discussion of Levantines or populations not found in Tazania in his post.
.
quote:
Originally posted by Punos_Rey:
Also found these tidbits interesting

"Western-Eurasian-related ancestry is pervasive in eastern Africa today (Pagani et al., 2012, Tishkoff et al., 2009), and the timing of this admixture has been estimated to be ∼3,000 BP on average (Pickrell et al., 2014). We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia. These results could be explained by migration into Africa from descendants of pre-pottery Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East." PR: Basal Eurasian?

"While these findings show that a Levant-Neolithic-related population made a critical contribution to the ancestry of present-day eastern Africans (Lazaridis et al., 2016), present-day Cushitic speakers such as the Somali cannot be fit simply as having Tanzania_Luxmanda_3100BP ancestry. The best fitting model for the Somali includes Tanzania_Luxmanda_3100BP ancestry, Dinka-related ancestry, and 16% ± 3% Iranian-Neolithic-related ancestry (p = 0.015). This suggests that ancestry related to the Iranian Neolithic appeared in eastern Africa after earlier gene flow related to Levant Neolithic populations, a scenario that is made more plausible by the genetic evidence of admixture of Iranian-Neolithic-related ancestry throughout the Levant by the time of the Bronze Age (Lazaridis et al., 2016) and in ancient Egypt by the Iron Age (Schuenemann et al., 2017)."

.
.
The authors of this article made sure to avoid using any archaeological data in their paper so thay could make many unsubstantiated statements like the following

quote:


These results could be explained by migration into Africa from descendants of pre-pottery Levantine farmers or alternatively by a scenario in which both pre-pottery Levantine farmers and Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East.

Here the authors bring up North Africa several times. In fact the authors as noted above claimed that the"Tanzania_Luxmanda_3100BP descend from a common ancestral population that lived thousands of years earlier in Africa or the Near East" ; or they were "descendants of pre-pottery Levantine farmers " Why do you want to avoid talking about issues in the article you posted?

.

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@Clyde Winters

I am not arguing. You are welcome to make your OWN thread criticizing the author. Go ahead.

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capra
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quote:
Originally posted by Elmaestro:
I'm not entirely sure but it looks like what little differences in Basal African Ancestry between the Mende and YRI is what defines how close other populations are to either of them. Mende having more Basal African Ancestry siglehandedly makes all other African populations closer to the Yorubans. Mbuti being representative of an early split just became less significant, as maybe even THEIR ancestry is drifted away considerably from the "ghost" African Ancestor. Yorubans as well as maybe all Bantu populations might have more Mbuti-like/(RHG) Admixture than the Mende.

~Reffering back to Patin 2017, elevated levels of RHG seems synonymous with scoring higher for Mbuti in comparison to Mota, It looks like YRI have admixture from Mbuti, and Basal African, and maybe more... this series of recombination is probably what shapes the west African genetic landscape, and that small amount of Archaic African means a lot...

yeah, looks like it. I would like to see a whole bunch more of those qpGraphs with different nodal populations, like with a proto-Pygmy population donating to others.

I know you can't really tack autosomal components on to uniparental markers, but looking at the latter we see some mid-levels that maybe ought to be the models. Mt hg L1 shared between West Africans and western Pygmies, L2 everywhere, L4 and L5 in the east. Y hg B2 practically everywhere outside West Africa. L0 + A1b1 can be accounted for in the East-South cline, L3 + E in the close-to-Eurasians node but I strongly suspect Mota ought to be mixed; L4b2 + B2b should not be conflated with L3 + E.

OT I am embarassed for Semitic Duwa right now, this is far below his usual standards of trolling.

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Elmaestro
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quote:
Originally posted by capra:
quote:
Originally posted by Elmaestro:
I'm not entirely sure but it looks like what little differences in Basal African Ancestry between the Mende and YRI is what defines how close other populations are to either of them. Mende having more Basal African Ancestry siglehandedly makes all other African populations closer to the Yorubans. Mbuti being representative of an early split just became less significant, as maybe even THEIR ancestry is drifted away considerably from the "ghost" African Ancestor. Yorubans as well as maybe all Bantu populations might have more Mbuti-like/(RHG) Admixture than the Mende.

~Reffering back to Patin 2017, elevated levels of RHG seems synonymous with scoring higher for Mbuti in comparison to Mota, It looks like YRI have admixture from Mbuti, and Basal African, and maybe more... this series of recombination is probably what shapes the west African genetic landscape, and that small amount of Archaic African means a lot...

yeah, looks like it. I would like to see a whole bunch more of those qpGraphs with different nodal populations, like with a proto-Pygmy population donating to others.

I know you can't really tack autosomal components on to uniparental markers, but looking at the latter we see some mid-levels that maybe ought to be the models. Mt hg L1 shared between West Africans and western Pygmies, L2 everywhere, L4 and L5 in the east. Y hg B2 practically everywhere outside West Africa. L0 + A1b1 can be accounted for in the East-South cline, L3 + E in the close-to-Eurasians node but I strongly suspect Mota ought to be mixed; L4b2 + B2b should not be conflated with L3 + E.

OT I am embarassed for Semitic Duwa right now, this is far below his usual standards of trolling.

Man I'm embarrassed for him too, however all that shit was legitimately funny... I was actually laughing out loud at my screen. In regards to some more robust qpGraphs, I'm working on it, I'm conflicted as to who should represent the root population, and how that'd effect coverage of Basal African lineages.
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Doug M
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MAKE YOUR OWN THREAD! I'm getting tired of repeating myself.

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[ 27. September 2017, 08:53 PM: Message edited by: Elite Diasporan ]

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BrandonP
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quote:
Originally posted by capra:
OT I am embarassed for Semitic Duwa right now, this is far below his usual standards of trolling.

In another ForumBiodiversity thread, he thanked this post:
 -
If he tries claiming he's objective and unbiased again, I will repost this screencap for all the world to see.

--------------------
Brought to you by Brandon S. Pilcher

My art thread on ES

And my books thread

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Askia_The_Great
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quote:
Originally posted by capra:

OT I am embarassed for Semitic Duwa right now, this is far below his usual standards of trolling. [/QB]

lol... I see you too are watching the nonsense on the other site. This is what happens when you refuse to admit to certain points like Beyoku said.

Anyways lets stay on topic folks. If you wanna address Duwa's meltdown then your welcomed to make another thread on here.

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Doug M
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quote:
Originally posted by Elite Diasporan:
But first shout outs to Djehuti. You were right on the money.

Anyways...
http://www.cell.com/cell/fulltext/S0092-86741731008-5

Many on the site Forumbiodiversity were certain this pastoralist would be more "Cushite-Like" with lineages like E-V22/M1 instead we get what I call "true Bantu Negroid" L2a1.

Here is the summary-
quote:
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.
Thoughts?
So are you saying you believe there is such a thing as a "true negro Bantustan" in Sub Saharan Africa that all Africans belong to? I mean this is not what the paper is saying so I don't understand your point? How is this significant? I mean who is shocked that black Africans would be found in "Sub Saharan" African DNA among any type of subsistance methods?

Please explain?

And I am not following threads from other forums. Why should we care about this on ES?

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the lioness,
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the lioness,
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quote:
Originally posted by Elite Diasporan:

http://www.cell.com/cell/fulltext/S0092-86741731008-5

Reconstructing Prehistoric African Population Structure
Pontus Skoglund, 2017

__________

Many on the site Forumbiodiversity were certain this pastoralist would be more "Cushite-Like" with lineages like E-V22/M1 instead we get what I call "true Bantu Negroid" L2a1.


quote:

We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia.


So in the thread topic article how did they determine the L21a Tanzanian woman of 3,100 BP was 38% Levantine?


quote:


Below another article but talking about African origins of L2a1


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515592/

60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2

Marina Silva,1 Farida Alshamali,1,2 Paula Silva,1,3,4 Carla Carrilho,5,6 Flávio Mandlate,5,7 Maria Jesus Trovoada,8,9 Viktor Černý,10 Luísa Pereira,a,1,3,4 and Pedro Soares1,11


L2a1 (26.5 ka in ML and 29.6 ka in BI) is the most complex sub-clade within L2a and it harbours lineages from all African regions, as well as lineages from other continents, including non-African branches, such as L2a1l2a (connected to Ashkenazi Jewish Diaspora35,36), and the exclusively European L2a1k37. Phylogenetic reconstruction of L2a1 is often difficult due to high levels of homoplasy. Major splits within L2a1 defined by homoplasic positions (143, 16189, 16192 and 16309) exist for parsimonious reconstruction purposes but will not be considered in the text. L2a1a has clearly a Western/Central African origin and distribution, with many sub-clades suggesting a recent Bantu migration southwards, and is hardly present in Eastern Africa. This pattern is also visible in L2a1c, L2a1f and L2a1i. L2a1e and the minor clade L2a1m exist essentially only in Western/Central Africa. L2a1l displays a similar pattern in sub-Saharan Africa, but with the peculiarity of a sub-branch present in Ashkenazi Jews, L2a1l2a35. L2a1b again shows an origin in Central Africa, but subclade L2a1b1a dating to 6.9 ka in ML is present in Southern Africa and has a few lineages in Eastern Africa (mainly Somalia). It might have moved earlier to the East in the Early Holocene and incorporated later by Bantu migrants. L2a1d splits into an Eastern African sub-clade (L2a1d1) at ~10.6 ka and L2a1d2 that shows a split between a Western African lineage and a Southern African clade dating to about 7 ka that contains the star-like L2a1d2a clade dating to 3.7 ka. Other clades show additional evidence of an early migration into Eastern Africa, like L2a1h and L2a1j. We detected a new clade specific to Somalia, L2a1r, at 7.3 ka. The clade L2a1 + 143 shows several basal Eastern African lineages (together with Near Eastern and Arabian lineages) that indicates a migration in the Early Holocene. Minor clades, namely L2a1g and L2a1q, are present in Bantu-speaking populations in the South and, although they were not detected in Western/Central Africa, their lower age suggest a direct involvement in the Bantu expansion.

L2a1b contains Somali lineages, whose founder age in Eastern Africa is 7.9 ka [1.5; 14.5] and the Eastern African L2a1d1 dates to 10.6 ka. L2a1h, probably with Eastern African origin, dates to 14.4 ka while L2a1r, a newly labelled Somali clade, dates to ~7.3 ka. Additionally, around 20% of Eastern African lineages cluster within the L2a1 + 143 branch (24.8 ka in ML). A founder age of this cluster suggests a migration time at 14.8 ka [10.2; 19.5], pointing to a migration in the Late Glacial or postglacial period. Overall, as predicted by HVSI-I data, most of the L2 lineages entered Eastern Africa between 15 and 7 ka.



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the lioness,
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quote:


Reconstructing Prehistoric African Population Structure
Pontus Skoglund

Agriculture was the foundation of the ancient Egyptian economy and vital to the lives of the people of the land. Agricultural practices began in the Delta Region of northern Egypt and the fertile basin known as the Faiyum in the Predynastic Period in Egypt (c. 6000 - c. 3150 BCE), but there is evidence of agricultural use and overuse of the land dating back to 8000 BCE.



yet >

quote:


https://www.ancient.eu/article/997/ancient-egyptian-agriculture/

Ancient Egyptian Agriculture


Agriculture was the foundation of the ancient Egyptian economy and vital to the lives of the people of the land. Agricultural practices began in the Delta Region of northern Egypt and the fertile basin known as the Faiyum in the Predynastic Period in Egypt (c. 6000 - c. 3150 BCE), but there is evidence of agricultural use and overuse of the land dating back to 8000 BCE.




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Elmaestro
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@lioness
What exactly are you trying to say, I'm lost.

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the lioness,
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copying error corrected in minute
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the lioness,
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CORRECTED VERSION quote 1
quote:


Reconstructing Prehistoric African Population Structure
Pontus Skoglund

Bantu-speaking agriculturalists originating in western Africa are thought to have brought farming to eastern Africa by ∼2,000 years BP (years before present, defined by convention as years before 1950 CE) and to southern Africa by ∼1,500 BP, thereby spreading the largest single ancestry component to African genomes today (Russell et al., 2014, Tishkoff et al., 2009). Earlier migration(s), which brought ancestry related to the ancient Near East (Lazaridis et al., 2016, Pagani et al., 2012, Pickrell et al., 2014), brought herding to eastern Africa by ∼4,000 BP (Marshall et al., 1984) and to southern Africa by ∼2,000 BP (Sadr, 2015).

yet >

quote:


https://www.ancient.eu/article/997/ancient-egyptian-agriculture/

Ancient Egyptian Agriculture


Agriculture was the foundation of the ancient Egyptian economy and vital to the lives of the people of the land. Agricultural practices began in the Delta Region of northern Egypt and the fertile basin known as the Faiyum in the Predynastic Period in Egypt (c. 6000 - c. 3150 BCE), but there is evidence of agricultural use and overuse of the land dating back to 8000 BCE.




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capra
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The crops grown in Egypt were temperate zone wheat, barley, etc, not suited to the tropics - eventually they were adapted to highlands of East Africa but it took a long time. The Eastern Bantu had tropical crops domesticated in the Sahel/Savanna zone - pearl millet, sorghum, cowpea, etc.

The Bantu didn't necessarily bring all - or any - of these crops to (the northern part of) East Africa originally. If they went through the rainforest growing yams and spreading oil-fruit trees, as may be the case, they may have switched over to completely different crops when they spread into drier parts of East Africa. But they did later carry this crop package south of Tanzania, by all evidence.

Oh hey this came out yesterday! Sorghum Domestication in Fourth Millennium BC Eastern Sudan: Spikelet Morphology from Ceramic Impressions of the Butana Group. Cool! Previously there was earlier evidence of domesticated sorghum in India than in Africa itself. The people growing this might have been among the ancestors of the Tanzania_Luxmanda_3100BP.

So looks like you are right, Lioness, at least kind of.

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Punos_Rey
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Thanks for the heads up Capra, brings back to mind Christopher Ehrets claims in 1996.

"Ancient Egyptian civilization was, in ways and to an extent usually not recognized, fundamentally African. The evidence of both language and culture reveals these African roots. The origins of Egyptian ethnicity lay in the areas south of Egypt. The ancient Egyptian language belonged to the Afrasian family (also called Afroasiatic or, formerly, Hamito-Semitic). The speakers of the earliest Afrasian languages, according to recent studies, were a set of peoples whose lands between 15,000 and 13,000 B.C. stretched from Nubia in the west to far northern Somalia in the east. They supported themselves by gathering wild grains. The first elements of Egyptian culture were laid down two thousand years later, between 12,000 and 10,000 B.C., when some of these Afrasian communities expanded northward into Egypt, bringing with them a language directly ancestral to ancient Egyptian. They also introduced to Egypt the idea of using wild grains as food." (Christopher Ehret (1996) "Ancient Egyptian as an African Language, Egypt as an African Culture." In Egypt in Africa Egypt in Africa, Theodore Celenko (ed), Indiana University Press)

Edit: also Capra, speaking of Barley..

"According to a widely accepted theory on barley domestication, wild barley (Hordeum vulgare ssp. spontaneum) from the Fertile Crescent is the progenitor of all cultivated barley (H. vulgare ssp. vulgare). To determine whether barley has undergone one or more domestication events, barley accessions from three continents have been studied (a) using 38 nuclear SSR (nuSSRs) markers, (b) using five chloroplast SSR (cpSSR) markers yielding 5 polymorphic loci and (c) by detecting the differences in a 468 bp fragment from the non-coding region of chloroplast DNA. A clear separation was found between Eritrean/Ethiopian barley and barley from West Asia and North Africa (WANA) as well as from Europe. The data from chloroplast DNA clearly indicate that the wild barley (H. vulgare ssp. spontaneum) as it is found today in the “Fertile Crescent” might not be the progenitor of the barley cultivated in Eritrea (and Ethiopia). Consequently, an independent domestication might have taken place at the Horn of Africa"

https://link.springer.com/article/10.1007%2Fs00122-007-0505-5

--------------------
 -

Meet on the Level, act upon the Plumb, part on the Square.

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Doug M
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Makes sense now and reflects what plenty of people have said here and elsewhere about cultivation of crops in Africa before the rise of agriculture in the Fertile Crescent. And I have mentioned this as part of a 'survival toolkit' that Africans carried into the Near East.....

But anyway here is another paper focusing on the "Bantu Cushite" interaction in terms of agriculture:

quote:

Although often marginalized or overlooked in the development of models for agricultural origins, Africa presents unique and theoretically informative case studies for global comparison. Eastern Africa is of particular interest for understanding farming expansions, not only because of its location encompassing the hypothesized migration routes of Bantu-speaking farmers and Cushitic- and Nilotic-speaking herders (Fig. 1), but also owing to its potentially early involvement in Indian Ocean trade, which brought novel domesticated plants and animals to its shores in prehistory. It has been suggested that eastern Africa's pre-agricultural communities had a role in dispersing vegetative crops such as banana (Musa spp.), taro (Colocasia esculenta), and Asian yam (Dioscorea alata) (all of which were first domesticated thousands of kilometers to the east in Sahul) across the tropical forests of Africa as early as the first millennium BCE (De Langhe, 2007; Blench, 2009).

http://www.sciencedirect.com/science/article/pii/S1040618216302890

quote:
For archaeologists, the story of how Near Eastern hunters and gatherers became farmers has become as familiar as a bedtime fable. Beginning as early as 11,000 B.C., people settled into villages and began cultivating wild grasses like rye, emmer wheat and barley. Over time, the genetic makeup of the plants changed, so they needed to be sown and tended in order to grow.

Cows, goats and sheep were domesticated over the next few thousand years, and then ceramics were developed to store food. This new way of life quickly swept across Europe and much of Asia. Soon, almost everyone was farming.

But not in Africa. As Dr. Katharina Neumann, an archaeobotanist at the J.W. Goethe University in Frankfurt, noted in the book ''Food, Fuel and Fields -- Progress in African Archaeobotany,'' published last year, archaeologists at several sites across sub-Saharan Africa have not found evidence of domesticated grains before 2000 B.C., suggesting that until then, people collected wild grains and did not plant their own.

While the first undisputed remains of domesticated cattle appear in the African archaeological record about 5900 B.C. at a site in Chad, other studies suggest that cattle were domesticated in the same region as early as 9,000 years ago.

http://www.nytimes.com/2004/07/27/science/african-pastoral-archaeologists-rewrite-history-of-farming.html?mcubz=1
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capra
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@PR - I can't access the barley paper, but looks interesting. I will check it out when I get the chance.

@Doug - thanks, I was thinking of posting the first one myself. The Panga ya Saidi site that Kenya_400BP is from was sampled in that paper. The Indian Ocean connection remains mysterious, though!

but maybe we should have a different thread for this

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the lioness,
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quote:


Reconstructing Prehistoric African Population Structure
Pontus Skoglund, 2017


We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia.


How do they get 38% of her ancestry is related to 10,000-year-old pre-pottery farmers of the Levant ?

How?

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capra
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See "Ancestry model and estimates with qpAdm" under Methods.

IIUC basically the qpAdm program runs f4 statistics, a measure of relatedness, between the target (in this case T_L_3100BP) and a set of outgroup populations. It then takes a set of potential source populations that you give it and creates virtual mixes from them. It calculates f4s between the virtual mix and the same set of outgroups, and compares them to the f4s determined for the actual target sample. A successful mix will have approximately matching f4 values, that is the same set of relationships with the outgroups as the target sample does.

So if for instance T_L_3100Bp was more closely related to West Africans than a mix of 38% PPNB and 62% Mota would be, that would show up in her having a stronger f4 with Mende than the mixture does. Or if she had not PPNB but say pure Basal Eurasian or super-Natufian or something like that, she would have a weaker f4 with Loschbour, Anatolia Neolithic, and so forth than the mix would have.

So it doesn't mean that she is literally a mix of Mota and PPNB but it can't really be something too crazy different from that. Look at the list of outgroup populations in the Methods to see what the constraints are.

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the lioness,
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Oh , I see the whole other section when you hit the methods tab

quote:

We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia.


quote:



METHODS

(excerpt)

Here, we used a model with 19 populations (Mbuti, Dinka, Mende, South_Africa_2000BP, Tanzania_Luxmanda_3100BP, Ethiopia_4500BP, Levant_Neolithic (PPNB), Anatolia_Neolithic, Iran_Neolithic, Denisova, Loschbour, Ust_Ishim, Georgian, Iranian, Greek, Punjabi, Orcadian, Ami, and Mixe), using previously published complete genomes (Fu et al., 2014, Lazaridis et al., 2014, Mallick et al., 2016, Meyer et al., 2012) and ancient DNA data enriched using the 1240k SNP set (Lazaridis et al., 2016, Mathieson et al., 2015) to maximize the power to infer admixture proportions for the ancient African populations. These populations, and in particular the ones from Africa, were chosen to capture major strands of ancestry and extremes in population differentiation found in sub-Saharan Africa (Figure 1)


Support for a single out-of-Africa founding population
Simple tree models suggest that non-African variation represented by Sardinian, English, Han Chinese and Japanese falls within the variation of African populations. To test whether non-Africans are indeed consistent with being descended from a homogeneous population that separated earlier from the ancestors of a subset of African populations – beyond the known effects of archaic admixture in non-Africans – we used African populations with little or no known West Eurasian mixture (South_Africa_2000BP, Mbuti, Biaka, Mende, Ethiopia_4500BP, Dinka) and tested whether they are consistent with being an unrooted clade with respect to a diverse set of non-Africans (Orcadian, Onge, Mixe, Motala_Mesolithic, Japanese, Anatolia_Neolithic) using qpWave (Patterson et al., 2012, Reich et al., 2012). We found that this model was consistent with the data (p = 0.53) (transition SNPs excluded to a final set of 110,507 transversion SNPs). Even when we add New Guinean highlanders to the set of non-Africans, the single-source model for the out-of-Africa founders is not rejected (p = 0.11).



wikipedia:

PPNB

Pre-Pottery Neolithic B (PPNB) is a Neolithic culture centered in upper Mesopotamia. It was typed by Kathleen Kenyon during her archaeological excavations at Jericho in the West Bank.

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I think Lioness is moreso questioning the date if anything, no true dating method for admixture was referenced if I remember correctly... in fact it'll be damn near impossible to date a single individuals Admixture event. However I'm guessing that the lack of Iranian ancestry is a key indicator. On that note, what do you guys think about the following... I managed to make some interesting qpGraphs but tbh, I'm baffled at this one. -No Outliers
Worst F-stat:
code:
                                fst:       fitted       estim        diff         std. err     Z score 
Lux Lev Eth Bar 0.000093 -0.003223 -0.003316 0.001744 -1.901

Seems like OOA might not be what I thought it was lol... not too sure yet if I failed to accommodate all the SSAn Admixture in Luxmanda with "NE_Nilotic" ...but for perspective, this model failed miserably. In my heart of hearts I wanna believe Luxmanda is in large 80%+ continental, I'll just let my biases out now.
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^^^@Capra your thoughts on this?
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 -


quote:
Originally posted by the lioness,:
Oh , I see the whole other section when you hit the methods tab

quote:

We found that the ∼3,100 BP individual (Tanzania_Luxmanda_3100BP), associated with a Savanna Pastoral Neolithic archeological tradition, could be modeled as having 38% ± 1% of her ancestry related to the nearly 10,000-year-old pre-pottery farmers of the Levant (Lazaridis et al., 2016), and we can exclude source populations related to early farmer populations in Iran and Anatolia.


quote:



METHODS

(excerpt)

Here, we used a model with 19 populations (Mbuti, Dinka, Mende, South_Africa_2000BP, Tanzania_Luxmanda_3100BP, Ethiopia_4500BP, Levant_Neolithic (PPNB), Anatolia_Neolithic, Iran_Neolithic, Denisova, Loschbour, Ust_Ishim, Georgian, Iranian, Greek, Punjabi, Orcadian, Ami, and Mixe), using previously published complete genomes (Fu et al., 2014, Lazaridis et al., 2014, Mallick et al., 2016, Meyer et al., 2012) and ancient DNA data enriched using the 1240k SNP set (Lazaridis et al., 2016, Mathieson et al., 2015) to maximize the power to infer admixture proportions for the ancient African populations. These populations, and in particular the ones from Africa, were chosen to capture major strands of ancestry and extremes in population differentiation found in sub-Saharan Africa (Figure 1)


Support for a single out-of-Africa founding population
Simple tree models suggest that non-African variation represented by Sardinian, English, Han Chinese and Japanese falls within the variation of African populations. To test whether non-Africans are indeed consistent with being descended from a homogeneous population that separated earlier from the ancestors of a subset of African populations – beyond the known effects of archaic admixture in non-Africans – we used African populations with little or no known West Eurasian mixture (South_Africa_2000BP, Mbuti, Biaka, Mende, Ethiopia_4500BP, Dinka) and tested whether they are consistent with being an unrooted clade with respect to a diverse set of non-Africans (Orcadian, Onge, Mixe, Motala_Mesolithic, Japanese, Anatolia_Neolithic) using qpWave (Patterson et al., 2012, Reich et al., 2012). We found that this model was consistent with the data (p = 0.53) (transition SNPs excluded to a final set of 110,507 transversion SNPs). Even when we add New Guinean highlanders to the set of non-Africans, the single-source model for the out-of-Africa founders is not rejected (p = 0.11).



wikipedia:

PPNB

Pre-Pottery Neolithic B (PPNB) is a Neolithic culture centered in upper Mesopotamia. It was typed by Kathleen Kenyon during her archaeological excavations at Jericho in the West Bank.

 -

" the skeleton H8 belonged to the African L3 lineage, this being the most prevalent African haplogroup found in present-day Near Eastern populations."

________________________________

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