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Author Topic: Ancient Tanzanian Pastoralist results... VERY interesting stuff!
capra
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quote:
Originally posted by Elmaestro:
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.

I doubt the admixture was at only one time and place anyway, but yeah, there is surely a more proximate source population, we just don't have a sample.

quote:
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...

Huh, I got nothing. Sometimes a list of D stats makes more sense to me than a qpGraph.

quote:
this model[/b] failed miserably. In my heart of hearts I wanna believe Luxmanda is in large 80%+ continental, I'll just let my biases out now.
So you can't put Mota 100% upstream of Bari, is Bari actually closer to South African then?
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Elite Diasporan
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This is the type of discussion I wanted to see. [Smile]
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Elmaestro
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quote:
Originally posted by capra:
Huh, I got nothing. Sometimes a list of D stats makes more sense to me than a qpGraph.

true, but having all is even better. However, if we really think about it,

"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.
"

-Skoglund 2017

I didn't see any reason for this postulation elaborated on in the study, luxmanda wasn't in any of the skeleton graphs either. The road block here is; Luxmanda will always fit between a contemporary non Admixed E.African (like Mota) and Levant_N... so how would we go about distinguishing whether Luxmanda is ancestral and to what degree, for instance 85% upsteam and 15% recombined from PPNB, which is a possibility.

quote:
So you can't put Mota 100% upstream of Bari, is Bari actually closer to South African then?
I Absolutely cannot... I'm thinking about A-M13 though, and what that Haplogroup can imply about pre-mota or even pre-PN2 population structure in east and Saharan Africa. I don't believe Nilotes are more San-like than Mota though.
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the lioness,
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http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23285/full

Internal diversification of non-Sub-Saharan haplogroups in Sahelian populations and the spread of pastoralism beyond the Sahara july 2017


Authors
Iva Kulichová,
Verónica Fernandes,
Alioune Deme,
Jana Nováčková,
Vlastimil Stenzl,
Andrea Novelletto,
Luísa Pereira,
Viktor Černý


Abstract

Background

Today, African pastoralists are found mainly in the Sahel/Savannah belt spanning 6,000 km from west to east, flanked by the Sahara to the north and tropical rainforests to the south. The most significant group among them are the Fulani who not only keep cattle breeds of possible West Eurasian ancestry, but form themselves a gene pool containing some paternally and maternally-transmitted West Eurasian haplogroups.
Materials and Methods

We generated complete sequences for 33 mitogenomes belonging to haplogroups H1 and U5 (23 and 10, respectively), and genotyped 16 STRs in 65 Y chromosomes belonging to haplogroup R1b-V88.
Results

We show that age estimates of the maternal lineage H1cb1, occurring almost exclusively in the Fulani, point to the time when the first cattle herders settled the Sahel/Savannah belt. Similar age estimates were obtained for paternal lineage R1b-V88, which occurs today in the Fulani but also in other, mostly pastoral populations. Maternal clade U5b1b1b, reported earlier in the Berbers, shows a shallower age, suggesting another possibly independent input into the Sahelian pastoralist gene pool.
Conclusions

Despite the fact that animal domestication originated in the Near East ∼ 10 ka, and that it was from there that animals such as sheep, goats as well as cattle were introduced into Northeast Africa soon thereafter, contemporary cattle keepers in the Sahel/Savannah belt show uniparental genetic affinities that suggest the possibility of an ancient contact with an additional ancestral population of western Mediterranean ancestry.

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Elmaestro
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Lioness do you think that the same population that brought V68 to South Europe or Mediterranean were conduits for V88 and H1 in SSA 8-7kya?
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the lioness,
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quote:
Originally posted by Elmaestro:
the same population that brought V68 to South Europe or Mediterranean

what's your reference ?

quote:
Originally posted by Elmaestro:
H1 in SSA 8-7kya


what's your reference ?
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Elmaestro
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For starters, the study you posted has V88 and H1 @ ~7kya in the Fulani.

 -
terminals 1-13 are Africans, 14 South Europe.


Also peep, V68* (V2009) found in Cameroon, Moroccan Berbers Sardinians and southern Italians (Trombetta 2015)

from Bakeda 2013-
quote:
Others, like sub-haplogroup U5b1b [34], sub-haplogroups H1 and H3 [20,35,36] and haplogroup V [37] seem to have reached North Africa from Iberia in a post-last glacial maximum expansion. In concordance, an ancient DNA study from Ibero-Maurusian bone remains from Taforalt in Morocco detected the presence of haplogroups U6, V, T and probably H, pointing to a Paleolithic genetic continuity in Northwest Africa [38]. Additionally, male lineages also provide support to a Paleolithic Asia to Africa back migration [39] with Holocene trans-Saharan spreads as testified by the haplogroup R-V88 distribution [40]. Other lineages, E-M81 [26] and E- M78 [41], seem to be of North African origin with Paleolithic and Neolithic expansions that reached surrounding areas. The presence of these clades in southwestern Europe has been attributed to trans-Mediterranean contacts **without involving the Levant**
I'm throwing this quote out here to give a little perspective... *notice how V88 is attributed to Near Eastern expansion during the Holocene!!

realquick, here's chiang 2016 on Sardinian population history
quote:
We were able to confirm a number of major features of previous analyses: the differentiation of Sardinia from mainland populations, the presence of high Neolithic farmer ancestry in Sardinia, and the presence of a small amount of sub-Saharan African admixture. Further, our analyses provide more detail regarding the isolation between Sardinia and the mainland. Our analysis of cross- coalescent rates suggest the population lineage ancestral to modern-day Sardinia was effectively isolated from the mainland European populations approximately 330 generations ago. This estimate should be treated with caution, but corresponds to approximately 9,900 years ago assuming a generation time of 30 years and mutation rate of 1.25x10-8 per basepair per generation
I mention that to point out the following...
 -

-Schroeder 2015; using an ancient AfroCarribean, they were able to get a coalesced age of 8.5 kya for the V88 split between Sards and Africans. We can effectively predict a timespan for which a lot of these relatively "inexplicable" clades were shuffled between Africa and Southern Europe, anywhere between 9000 and 5000 years ago. And there is detectable substructure among the "Eurasian" contributions to Fulani though the Kulichova et al 2017 article you posted above glosses over this.(because their main concern was Eurasians tbh, particularly potential European genetic and cultural contributions and not the African populations themselves.. ¯\_(ツ)_/¯ ) ...Not to mention Habers dates for non African Admixture and V88.

quote:
" ~The number of samples is shown on each branch tip.We estimate that the Chadian R1b emerged 5,700–7,300 ya, whereas most European R1b haplogroups emerged 7,300–9,400 ya. The African and Eurasian lineages coalesced 17,900–23,000 ya."
^ His broad coalescent age is important because his model was going off the assumption that V88 was acquired from the near east. However what he unintentionally does is provide evidence for an isolated Eurasian branch being related to the African variety. Which we have evidence for. -see above.
-Sards split from Europeans prior to the Coalesced age of V88 in the latter populations
-SSAfrican V88 coalesces with Sardinian V88 after the supposed Isolation.
-North Africa is between SSA and Sardinia
-European signatures are weak in SSA African populations, other than the handful of Fula(or any other Africans) which recent European or even North African ancestry.

And we should all keep in mind the presence of ancient North African DNA now and how that keeps suggestions such as Bakeda's (quoted above) in check.

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the lioness,
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Your argument is good I haven't been following V68.
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the lioness,
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Also see:

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22236/abstract

Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel

Authors
Jana Bučková,
Viktor Černý,
Andrea Novelletto
First published: 4 March 2013


 -

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Swenet
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quote:
Originally posted by Elmaestro:
For starters, the study you posted has V88 and H1 @ ~7kya in the Fulani.

quote:
Originally posted by Elmaestro:
Also peep, V68* (V2009) found in Cameroon, Moroccan Berbers Sardinians and southern Italians (Trombetta 2015)

quote:
Originally posted by Elmaestro:
Other lineages, E-M81 [26] and E- M78 [41], seem to be of North African origin with Paleolithic and Neolithic expansions that reached surrounding areas. The presence of these clades in southwestern Europe has been attributed to trans-Mediterranean contacts **without involving the Levant**

quote:
Originally posted by Elmaestro:
-Sards split from Europeans prior to the Coalesced age of V88 in the latter populations
-SSAfrican V88 coalesces with Sardinian V88 after the supposed Isolation.
-North Africa is between SSA and Sardinia

-European signatures are weak in SSA African populations, other than the handful of Fula(or any other Africans) which recent European or even North African ancestry.

Wait, so you subscribe to neolithic north-south trans-mediterranean contacts now? Didn't you strongly reject north-south Mediterranean contacts involving some EEF subgroups and the ancestors of Egyptians as "Hamiticism"?
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Elmaestro
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quote:
Originally posted by Swenet:
quote:
Originally posted by Elmaestro:
For starters, the study you posted has V88 and H1 @ ~7kya in the Fulani.

quote:
Originally posted by Elmaestro:
Also peep, V68* (V2009) found in Cameroon, Moroccan Berbers Sardinians and southern Italians (Trombetta 2015)

quote:
Originally posted by Elmaestro:
Other lineages, E-M81 [26] and E- M78 [41], seem to be of North African origin with Paleolithic and Neolithic expansions that reached surrounding areas. The presence of these clades in southwestern Europe has been attributed to trans-Mediterranean contacts **without involving the Levant**

quote:
Originally posted by Elmaestro:
-Sards split from Europeans prior to the Coalesced age of V88 in the latter populations
-SSAfrican V88 coalesces with Sardinian V88 after the supposed Isolation.
-North Africa is between SSA and Sardinia

-European signatures are weak in SSA African populations, other than the handful of Fula(or any other Africans) which recent European or even North African ancestry.

Wait, so you subscribe to neolithic north-south trans-mediterranean contacts now? Didn't you strongly reject north-south Mediterranean contacts involving some EEF subgroups and the ancestors of Egyptians as "Hamiticism"?

Actually I was against the whoooole premise that there was an "Indigenous North African element" all together... But a few months ago I saw a few patterns that convinced me other wise, around the time when I started saying that there was no Basal Eurasian...

However I'm still not sold on the premise of Eurasian Farmers being responsible for physical variation in Africa and the eventual development of Ancient Egyptian culture etc. (...which is specifically what I'd refer to as Hamiticism.)

-But yeah, (though I don't remember neglecting trans Mediterranean contact). I view it differently now...

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Swenet
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quote:
Originally posted by Elmaestro:
But yeah, (though I don't remember neglecting trans Mediterranean contact). I view it differently now...

I could have sworn you denied African ancestry in Aegean Neolithic just days ago (i.e. during my conversation with Polako), when I was literally trying to make the same argument you're making right now (i.e. direct maritime migration involving V68 and V257).

Am I missing something? If not that, what did you object to a couple of days ago?

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Elmaestro
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Oh! I couldn't find any evidence for significant African contribution to Lazaridis' Mycenaean, Minoan and Greek samples ...So I conceded that point to them. ¯\_(ツ)_/¯

But just so you know...Before on ABF When the Greek samples showed a lil bit of SSA.. I made a snarky remark about that being "surprising" to some people. When the Neolithic Moroccan paper dropped polako came at me personally, then made a general comment in public which I felt was aimed at me, cuz it echoed what he said to me.. But I personally wanted to crush him in public, so before I did any of that I gave him that point about the Neolithic Greeks, so that he wouldn't dwell on that as opposed to the more important stuff.

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the lioness,
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quote:
Originally posted by Elmaestro:
Lioness do you think that the same population that brought V68 to South Europe or Mediterranean were conduits for V88 and H1 in SSA 8-7kya?

As we see on the chart the Fulani are primarily E carriers.
Some are R1b carriers

Essential reading on this complex topic is behind a pay wall ( but I have read it) particularly the discussion section

________________________________________________

Multiple and Differentiated Contributions to the Male Gene Pool of Pastoral and Farmer Populations of the African Sahel

https://www.researchgate.net/publication/235787499_Multiple_and_Differentiated_Contributions_to_the_Male_Gen
Jana Bučková,
Viktor Černý,
Andrea Novelletto
First published: 4 March 2013


While the majority of the mtDNA gene pool of the Fulani popula- tion belongs to the West African gene pool, it also includes lineages such as U5 and J1b (Cerezo et al., 2011; Cerny; et al., 2006, 2011) that must have been introduced in their population via North Africa, perhaps together with R1b. Haplogroup U5b1b, with a coales- cence age 􏰂8.6 ka and a presence in West Africa, the West Mediterranean and even in North Europe (Achilli et al., 2005) provides a good argument for such reason- ing. Last but not least, the 13,910C>T variant enabling the lactase persistence phenotype (Lokki et al., 2011) is one the Fulani nomads also share with Europeans.
Our data show that R1b-M343 does not prevail in Chadic speaking groups as reported previously by Cruciani et al. (2010a). In fact, we found this haplogroup exclusively in the Fulani pastoralists’ gene pool and not in the today sedentary Chadic populations.

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sudaniya
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What percentage of EFF ancestry did the ancient Egyptians supposedly have?

--------------------
National sovereignty is sacrosanct

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Djehuti
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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?
Sorry for the late response. I just got through reading the paper and it's really nothing surprising. A lot of genetic diversity has been lost since the Holocene not only in Africa but throughout the world via the spread of food producing populations which either replaced or subsumed other groups.

By the way Elite, E-V22/M1 is a male lineage found in the Y-chromosome while L2a1 is a female lineage found in mitochondria. The Luxmanda specimen is female so she doesn't have any Y chromosome. That said, it is interesting to note that most of the ancient Y chromosomes found from males in the sites are A or B and not E derived.

I have to agree with Punos Rey that this common ancestry that Luxmanda had associated with the neolithic Levant may very well be the so-called "basal Eurasian", and that such ancestry may very well be indigenous to Africa instead of Eurasia. Check out Swenet's blog page on that topic here.

As far as Somali having 16% ± 3% Iranian-Neolithic-related ancestry, this too is no surprise considering the presence of paternal lineage hg T in Somalia and other parts of the Horn. T is derived from hg LT and is a sibling of hg L which is predominantly found in India and Iran. Interestingly while T is also found in India and traces are found throughout western Eurasia, the highest frequency is found in the Horn.

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Djehuti
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One thing I forgot to mention is that it is of utmost importance not only of understanding the genetic landscape of Africa but also Southwest Asia as well and this includes not only the Levant but also Arabia. I personally believe Arabia is the missing link between what is African and 'Eurasian'. I can't stress S.O.Y. Keita's point enough that paleolithic hunter-gatherers have been moving back and forth between North Africa and Southwest Asia that it would be difficult to ascertain which lineages are truly 'Eurasian'. Hence "basal Eurasian" which I believe to be a parallel ancestral group originating in Africa but descending from the same pre-OOA populations. I have read excerpts from old studies and literature including those cited by Dana describing ancient skeletal remains in Arabia displaying "negroid" or "African" features.
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Elmaestro
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quote:
Originally posted by sudaniya:
What percentage of EFF ancestry did the ancient Egyptians supposedly have?

Can you Elaborate on what you specifically mean by EEF, cuz I have the same exact question, Eurasian farmers that actually came from Eurasia, or North Africans that didn't go no where but makes up a portion of the current southern European and Near eastern genepool? I'd like to believe the former was negligible earlier but increased over time, as for the Latter, atm, your guess is as good as mines, could be 100%, but Idk how much sense that would make archaeologically.

@Djehuti
at this point, we might as well treat the term "Basal Eurasian" as a misnomer, really suggesting "African Affinity". cuz the only thing these carriers have in common is African Affinity... And it's not even like a singular African population can best fit the mold.

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Doug M
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Just note that most "Africa wide" studies of DNA omit populations in the Sahel, including the Fulani, the populations of Southern Algeria, Northern Mali, Mauritania, Northern Sudan and so forth. And when they do study the DNA of these populations, they are treated as a "distinct group" of their own, in other words, not included in North Africa and not included as "Sub Saharan". Just more games being played with the data.....

quote:

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

African genetic diversity is still incompletely understood, and vast regions in Africa remain genetically undocumented. Chad, for example, makes up ∼5% of Africa’s surface area, and its central location, connecting sub-Saharan Africa with North and East Africa, positions it to play an important role as a crossroad or barrier to human migrations. However, Chad has been little studied at a whole-genome level, and its position within African genetic diversity is not well known. With 200 ethnic groups and more than 120 indigenous languages and dialects, Chad has extensive ethnolinguistic diversity.1 It has been suggested that this diversity can be attributed to Lake Chad, which has attracted human populations to its fertile surroundings since prehistoric times, especially after the progressive desiccation of the Sahara starting ∼7,000 years ago (ya).

Important questions about Africa’s ethnic diversity are the relationships among the different groups and the relationships between cultural groups and existing genetic structures. In the present study, we analyzed four Chadian populations with different ethnicities, languages, and modes of subsistence. Our samples are likely to capture recent genetic signals of migration and mixing and also have the potential to show ancestral genomic relationships that are shared among Chadians and other populations. An additional major question relates to the prehistoric Eurasian migrations to Africa: what was the extent of these migrations, how have they affected African genetic diversity, and what present-day populations harbor genetic signals from the ancient migrating Eurasians? We have previously reported evidence of gene flow from the Near East to East Africa ∼3,000 ya, as well as subsequent selection in Ethiopians on non-African-derived alleles related to light skin pigmentation.

snip

Multiple Eurasian Admixtures in Africa after 6,000 ya

We have previously reported massive gene flow ~3,000 ya from Eurasians to Ethiopian populations.4 Here, we reassess the presence of Eurasian ancestry in Africa by using f3 statistics25 in the form of f3:X; Eurasian, Yoruba, where a negative value with a Z score < -4 indicates that X is a mixture of Africans and Eurasians. We found, as expected, that most Ethiopians are a mixture of Africans and Eurasians. An exception is the Gumuz population, where f3: Gumuz; Eurasian, Yoruba is always positive. The Gumuz language belongs to the Nilo-Saharan family, which could have isolated the Gumuz from the Afro-Asiatic-speaking Ethiopians. However, we found that the Toubou in Chad, who also speak a Nilo-Saharan language, are a mixture of Africans and Eurasians, making f3:Toubou; Eurasian, Yoruba always significantly negative. This suggests that the impact of Eurasian migrations today extends beyond East Africa and the Afro-Asiatic-speaking populations.

http://www.sciencedirect.com/science/article/pii/S0002929716304487


 -

They say they have little DNA from Chad and other African populations but they are quick to claim that "Eurasians" migrated all the way into Central Africa? Seriously? Where are the other surrounding African populations included as part of this study? Note the primary populations used for comparison: Yoruba (the so called pure sub saharans reference population used in most of these studies), Ethiopians like the Ahmara and then they go way off to Greece and Turkey. No Fulani included, No Tuareg included. No Northern Nigerians included, No populations in Niger included. No Sudanese (Beja, "nubians", Darfurians, Nuer, Dinka, etc). No populations surrounding Chad were included. But this is the game they play with all these papers. By now any Africa wide genomic study should inclcude ALL populations of Africa not certain hand picked populations used over and over again.

And not to mention lets not talk about any DNA from ancient remains in Chad compared to moderns... which is standard for most of these types of DNA studies, except in Africa. Of course they will claim that they cant find any ancient sites and remains in Chad for whatever reason.

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Clyde Winters
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Mod

Like I said create your OWN thread. You're free to do so. Final warning
.

[ 07. October 2017, 06:08 PM: Message edited by: Elite Diasporan ]

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

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@Doug
In a perfect world where you got your way as far as how we do research, what results would you expect to see? This isn't an essay question btw, can you keep it short.

EDIT oh fuck, look at what you started ....all because you're afraid to actually read a fucking paper.

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Djehuti
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quote:
Originally posted by Elmaestro:

Can you Elaborate on what you specifically mean by EEF, cuz I have the same exact question, Eurasian farmers that actually came from Eurasia, or North Africans that didn't go no where but makes up a portion of the current southern European and Near eastern genepool? I'd like to believe the former was negligible earlier but increased over time, as for the Latter, atm, your guess is as good as mines, could be 100%, but Idk how much sense that would make archaeologically.

If I'm not mistaken EEF means Early European Farmer which is comprised of Neolithic Near Easterners and Western Hunter Gatherers.

quote:
@Djehuti
at this point, we might as well treat the term "Basal Eurasian" as a misnomer, really suggesting "African Affinity". cuz the only thing these carriers have in common is African Affinity... And it's not even like a singular African population can best fit the mold.

Unfortunately we do not yet have the smoking gun so to speak in the form of skeletal remains in Africa yielding the 'Basal Eurasian' component at significant enough frequency which is why they still use the term "Eurasian". This despite the fact that there are skeletal remains in Southwest Asia (both Levant and Arabia) displaying African features.
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quote:
Originally posted by sudaniya:
What percentage of EFF ancestry did the ancient Egyptians supposedly have?

While we do have records of European populations like the Greeks and Sea Peoples settling in northern Egypt during the late dynastic period, I suspect most of the Eurasian ancestry in AE would have come from Levantine rather than European sources. And I don't think we have enough aDNA data yet to say for sure how much Eurasian vs indigenous North & sub-Saharan African ancestry the AE throughout time and space had. We might have to wait and see on this one.
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Elite Diasporan
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quote:
Originally posted by Djehuti:
Sorry for the late response. I just got through reading the paper and it's really nothing surprising. A lot of genetic diversity has been lost since the Holocene not only in Africa but throughout the world via the spread of food producing populations which either replaced or subsumed other groups.

No prob. Just glad you can join. And yeah a lot of genetic diversity has been lost sadly. I'm pretty sure those food producing populations were able to become more larger and dominate other groups. But its surprising to me personally in that the maternal lineage for the Tanzanian pastoralist is not a "Southern Cushite" one.


quote:
Originally posted by Djehuti:
By the way Elite, E-V22/M1 is a male lineage found in the Y-chromosome while L2a1 is a female lineage found in mitochondria. The Luxmanda specimen is female so she doesn't have any Y chromosome. That said, it is interesting to note that most of the ancient Y chromosomes found from males in the sites are A or B and not E derived.

I am completely aware of the bolded. Again what I meant was that people on Forumbiodiversity were HOPING to see more "Southern Cushite-like" lineages for Luxmanda like M1 or L0 for example. Instead they got L2a1 which they consider "true Negroid" and have been ignoring this study ever since. They were hoping this female would be representative for Upper Egyptians. While not from FBD, Razid Khan was one of those Euronuits praying she would be a Cushite-Levant type. Basically what they REALLY wanted was almost "pure" Eurasians in Southeast Africa. Instead they got the TOTAL OPPOSITE not even Cushite types. The males mainly being A or B only makes it WORSE for them.
https://mobile.twitter.com/razibkhan/status/881895944710651904

quote:
Originally posted by Djehuti:

I have to agree with Punos Rey that this common ancestry that Luxmanda had associated with the neolithic Levant may very well be the so-called "basal Eurasian", and that such ancestry may very well be indigenous to Africa instead of Eurasia. Check out Swenet's blog page on that topic here.

Don't quote me on this but there have been theories on here that the Hadza could carry some Basel Eurasian but it was thrown out the window because it was a theory that was just played around with. Luxmanda seems to occupy the same location as the Hadza, but again dont quote me on this. And yeah i read Swenet's blog before may give it another read.

quote:
Originally posted by Djehuti:

As far as Somali having 16% ± 3% Iranian-Neolithic-related ancestry, this too is no surprise considering the presence of paternal lineage hg T in Somalia and other parts of the Horn. T is derived from hg LT and is a sibling of hg L which is predominantly found in India and Iran. Interestingly while T is also found in India and traces are found throughout western Eurasia, the highest frequency is found in the Horn.

Never knew the highest frequencies were found in the Horn. Learn new stuff everyday.
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Elite Diasporan
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quote:
Originally posted by Tyrannohotep:
While we do have records of European populations like the Greeks and Sea Peoples settling in northern Egypt during the late dynastic period, I suspect most of the Eurasian ancestry in AE would have come from Levantine rather than European sources. And I don't think we have enough aDNA data yet to say for sure how much Eurasian vs indigenous North & sub-Saharan African ancestry the AE throughout time and space had. We might have to wait and see on this one.

In your opinion what do you think this study might say for Upper Egyptians. I mean the timeline for these pastoralist is 3,000 years ago.
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Doug M
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quote:
Originally posted by Elmaestro:
@Doug
In a perfect world where you got your way as far as how we do research, what results would you expect to see? This isn't an essay question btw, can you keep it short.

EDIT oh fuck, look at what you started ....all because you're afraid to actually read a fucking paper.

The point is you are seeing "false positives" based on selective DNA sampling and comparisons.

And it isn't a "perfect world" which is why I don't pretend these papers are really pushing anything more than propaganda.... ie. Eurasians overran North Africa and thus limiting "true African" DNA lineages to the "Sub Saharan" bantustan lineages...

The TL;DR Bottom line African genetic history should not be modeled on or based on "Eurasian" anything. The roots of and origins of farming included.

quote:

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). However, the population structure of Africa prior to the expansion of food producers (pastoralists and agriculturalists) remains unknown (Busby et al., 2016, Gurdasani et al., 2015, Patin et al., 2017). 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).

This is nothing more than a rehashing of the old Bantustan model of African DNA. It doesn't go back more than 10 thousand years and doesn't discuss the antiquity of African DNA prior to that.


 -

Not to mention the fact that Africans have been practicing all sorts of subsistence strategies, including collecting wild grains and herding wild cattle and livestock since LONG BEFORE any Eurasian back migration during the Neolithic. In fact I would argue that the movement of Saharan populations after the drying of the Sahara 10,000 years ago is a key spark for the arrival of the Neolithic in the "Near East".

quote:

There are essentially three archaeologically-based models for the domestication of cattle in North Africa. Wendorf et al. (2001) argue for domestication in the 9th millennium BC, pointing to their reconstruction of the ecology of the Nabta Play – Bir Kiseiba region and to diminishing skeletal size; there is minimal if any input from Near Eastern cattle later on. Andrew Smith’s (2005) model states that the inhabitants of the NP region were hunter-gatherers prior to the late 6th millennium BC and that all the cattle and ovicaprids came from the Near East via the Red Sea coast. My (2007) model hypothesises that anatomical domestication occurred ca 6300 BC, around the time that ovicaprids were introduced into the Eastern Sahara and this may well have included cattle too, and that they were incorporated into and transformed the economy & social structures of the inhabitants of the Nabta Playa-Bir Kiseiba area who had previously been managing some small numbers of wild cattle. It is this managing of wild cattle which could have been a source for the Y2 introgression and the mixed mtDNA results seen to date.

Maria Gatto (2011), however, notes that the early Nabta Playa-Bir Kiseiba pottery is part of the same tradition as the early Kerma region pottery, augmenting Donatella Usai’s (2005) analysis of the stone tools from Nabta Playa in reaching a similar conclusion. There are also currently no known earlier instances of Bos primigenious in the Kerma region, which argues in favour of Honegger’s cattle having been under human control. This is taken by Honegger and Gatto as being supportive of the early domestication model of Wendorf & Schild, i.e. that the cattle were brought to the Kerma region from Nabta Playa-Bir Kiseiba through pastoralist contact with more settled hunter-forager communities living along the Nile.

However, the issue is not so cut and dried. If the criticisms of the reconstruction of the Nabta Playa-Bir Kiseiba ecology are valid and a limited degree of herd management was occurring, possibly similar to the less dangerous Barbary sheep in the Acacus Mountains around this time (di Lernia, 2001), there is no valid reason why some of these cattle would not have been exchanged and ended up in the more favourable environment in the Nile Valley.

What we may be witnessing in fact are two or more centres of morphological domestication occurring, a phenomenon which frankly should not be surprising. Perhaps as part of re-evaluating our epistemological and theoretical approaches to early cattle domestication in North-East Africa, we should also consider discontinuing the antiquated use of imported terms such as Neolithic (Gatto, 2011; Wengrow 2006) and instead continue developing appropriate regionalised archaeolological traditions (cf. Garcea, 2004). This is a wake-up call for North-East Africanists more broadly to better critically engage with the trends, methods and theories being developed elsewhere both on the African continent and elsewhere, as many who are fauna and faunal specialists already do.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3783853/

quote:



Researchers at the Organic Geochemistry Unit in the University of Bristol's School of Chemistry, working with colleagues at Sapienza, University of Rome and the Universities of Modena and Milan, studied unglazed pottery dating from more than 10,000 years ago, from two sites in the Libyan Sahara.

The invention of cooking has long been recognised as a critical step in human development.

Ancient cooking would have initially involved the use of fires or pits and the invention of ceramic cooking vessels led to an expansion of food preparation techniques.

....
Detailed investigations of the molecular and stable isotope compositions showed a broad range of plants were processed, including grains, the leafy parts of terrestrial plants, and most unusually, aquatic plants.

The interpretations of the chemical signatures obtained from the pottery are supported by abundant plant remains preserved in remarkable condition due to the arid desert environment at the sites.

The plant chemical signatures from the pottery show that the processing of plants was practiced for over 4,000 years, indicating the importance of plants to the ancient people of the prehistoric Sahara.

Dr Julie Dunne, a post-doctoral research associate Bristol's School of Chemistry and lead author of the paper, said: "Until now, the importance of plants in prehistoric diets has been under-recognised but this work clearly demonstrates the importance of plants as a reliable dietary resource.

"These findings also emphasise the sophistication of these early hunter-gatherers in their utilisation of a broad range of plant types, and the ability to boil them for long periods of time in newly invented ceramic vessels would have significantly increased the range of plants prehistoric people could eat."

https://phys.org/news/2016-12-earliest-evidence-cooked-ancient-pottery.html

And of course we cannot pretend that the arrival of the Neolithic is the basis of ancient African DNA going back 300,000 years which is absurd. But that is precisely what they are doing with this paper....

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Swenet
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quote:
Originally posted by Tyrannohotep:
While we do have records of European populations like the Greeks and Sea Peoples settling in northern Egypt during the late dynastic period, I suspect most of the Eurasian ancestry in AE would have come from Levantine rather than European sources. And I don't think we have enough aDNA data yet to say for sure how much Eurasian vs indigenous North & sub-Saharan African ancestry the AE throughout time and space had. We might have to wait and see on this one.

True. Which makes it all the more ironic that predynastics are, phenotypically, closer to most EEF subgroups than to Natufians and PPN.

I think this discrepancy is partly due to what I told Polako about E-V68 and E-V257, partly because of the unique pre-Natufian genetic makeup of the Levant, and partly because the autosomal signature associated with the Neolithization of North Africa was not typically Levantine. R1b-V88, although ultimately of eastern Eurasian origin, seems more consistent with EEF-related ancestry around the time it was introduced to North Africa (not with Levantine ancestry).

In fact, the apparent presence of R1b in the Levant in post-PPN times jibes well with the trend of homogenization and the spread of EEF-like ancestry in the Mediterranean basin. So, for instance, the Natufian-PPN transition is associated with roughly as much EEF-like input as the IAM-KEB transition is. This suggests that post-PPN populations in the Levant are likely to have even more EEF-like input than PPN do. Relevance? The R1b carriers who introduced domesticates to Egypt ~7kya apparently belonged to this EEF-admixed post-PPN population.

BTW, this is also why I'm very sceptical of claims that the non-SSA ancestry in Africa (e.g. Luxmanda) is actually PPN. It's anachronistic as it does not fit the aforementioned trend of homogenization. Luxmanda's so-called PPN could easily be something EEF-related + various components of which some are African, because that is exactly what PPN is also. I think when predynastics are sampled, their non-SSA ancestry will show a preference for PPN and Natufians (compared to EEF). But, taken literally, this is similarly bogus for all the aforementioned reasons.

quote:
Originally posted by Djehuti:
Check out Swenet's blog page on that topic here.[/QB]

When I have time I will make a new post about Basal Eurasian because I understand it much better now.
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Ish Gebor
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quote:
Originally posted by the lioness,:
Your argument is good I haven't been following V68.

Sure you haven't. [Big Grin] [Frown] [Embarrassed]


quote:



Within E-M35, there are striking parallels between two haplogroups, E-V68 and E-V257. Both contain a lineage which has been frequently observed in Africa (E-M78 and E-M81, respectively) [6], [8], [10], [13]–[16] and a group of undifferentiated chromosomes that are mostly found in southern Europe (Table S2). An expansion of E-M35 carriers, possibly from the Middle East as proposed by other Authors [14], and split into two branches separated by the geographic barrier of the Mediterranean Sea, would explain this geographic pattern. However, the absence of E-V68* and E-V257* in the Middle East (Table S2) makes a maritime spread between northern Africa and southern Europe a more plausible hypothesis. A detailed analysis of the Y chromosomal microsatellite variation associated with E-V68 and E-V257 could help in gaining a better understanding of the likely timing and place of origin of these two haplogroups.

--Beniamino Trombetta, Fulvio Cruciani et al. (2011)

A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms

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capra
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quote:
Originally posted by Swenet:
BTW, this is also why I'm very sceptical of claims that the non-SSA ancestry in Africa (e.g. Luxmanda) is actually PPN. It's anachronistic as it does not fit the aforementioned trend of homogenization. Luxmanda's so-called PPN could easily be something EEF-related + various components of which some are African, because that is exactly what PPN is also.

I haven't seen any stats with Natufians for the ancient East Africans, but apparently Maasai and Somalis are equidistant between PPNB and Natufians. There's no Natufian in the qpAdm population set, so maybe something more toward Natufian than PPNB would fit. I'd like to see that stats for them and ancient Egyptians, and of course for IAM when the genomes are released.

The biggest outlier for Luxmanda is with South_Africa_2000BP though, possibly meaning Mota is too southern on the East-South Africa cline as a reference; maybe Luxmanda has a bunch of ancestral East African ancestry from further north?

Looking at the outlier stats for the qpAdm models, most of them are minor and explicable but there are a couple of really weird ones. Like it appears that Ju|'hoan have (non-literal) anti-Denisovan and Mbuti anti-Iran Neolithic. [Big Grin] [Confused]

From what I understand PPNB didn't really expand into Egypt, there's some influence - livestock obviously, Helwan-type points, but doesn't look like a wholesale migration really? But I may have picked that up from some unreliable source, like Afrocentrists. [Wink]

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Elmaestro
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quote:
Originally posted by Doug M:
The point is you are seeing "false positives" based on selective DNA sampling and comparisons.

And it isn't a "perfect world" which is why I don't pretend these papers are really pushing anything more than propaganda.... ie. Eurasians overran North Africa and thus limiting "true African" DNA lineages to the "Sub Saharan" bantustan lineages...

The TL;DR Bottom line African genetic history should not be modeled on or based on "Eurasian" anything. The roots of and origins of farming included.

Ok... let's try again, what do you expect to see in the available ancient genomes? Which populations, ancient or extant do you desire to be Analyzed? And when they are, what exactly do you expect from the outcome?
^Start here, never mind the "BASAL this" or "Eurasian that" ...just please, start from here^ and help contribute to the progression of Afrocentered freelance research please.

I find it funny that you complain about African not only being Bantoid or SSA or whatever, but little do you know Indigenous North African might be closest to ProtoBantu, not only that, I can tell you haven't so much as read the Abstract from Fregel 2017 operating on Ancient North African DNA, maybe if you did, you can occupy ground to debate on.

quote:
Originally posted by Djehuti:
If I'm not mistaken EEF means Early European Farmer which is comprised of Neolithic Near Easterners and Western Hunter Gatherers.

Unfortunately we do not yet have the smoking gun so to speak in the form of skeletal remains in Africa yielding the 'Basal Eurasian' component at significant enough frequency which is why they still use the term "Eurasian". This despite the fact that there are skeletal remains in Southwest Asia (both Levant and Arabia) displaying African features.

It doesn't matter what it's called(Basal Eurasian), what does matter however, is the fact that we wont find a smoking gun... For instance to reiterate on my previous point, Hotu, draws closer or shows signatures related to Senegambians.. Natufians to a pseudo ~East African with low San HG, and CHGs to Nilotes. All three of these populations consistently show SSA signatures and score very high for Lazaridis' Basal Eurasian... How can a singular African population accommodate for all this variation?

Swenet makes a good point...
quote:
BTW, this is also why I'm very sceptical of claims that the non-SSA ancestry in Africa (e.g. Luxmanda) is actually PPN. It's anachronistic as it does not fit the aforementioned trend of homogenization. Luxmanda's so-called PPN could easily be something EEF-related + various components of which some are African, because that is exactly what PPN is also. I think when predynastics are sampled, their non-SSA ancestry will show a preference for PPN and Natufians (compared to EEF). But, taken literally, this is similarly bogus for all the aforementioned reasons.
I cosign the Model, but to me whatever falls inline with being EEF-like is simply NorthAfrican Ancestry shared between European Neolithic Groups... Which I believe is supported by the ruling out of Anatolian Admixture (Skoglund 2017). the remainder of Luxmandas ancestry not shared with African groups in the paper is more related to the Near east (some if not all is actually due to admixture FMPOV)... regardless, this doesn't happen with a archetypal African Basal Eurasian subgroup existing, unless its North African... how does that Idea hold up with NAfrican aDNA, KEB can't be Basal Eurasian like, ...IAM, maybe, however, if you can prove introgression from Ibermaurasians and Model the remaining outgroup as both African but not SSAn... But once again, I don't know how well this is supported by archaeology
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Elite Diasporan
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THIS is the DAMN discussion I wanted!!! thank you Capra, Elmaestro, DJ, Swenet and Lioness. [Smile]

If we keep this up we can turn around the Egyptology section.

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Swenet
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quote:
Originally posted by capra:
quote:
Originally posted by Swenet:
BTW, this is also why I'm very sceptical of claims that the non-SSA ancestry in Africa (e.g. Luxmanda) is actually PPN. It's anachronistic as it does not fit the aforementioned trend of homogenization. Luxmanda's so-called PPN could easily be something EEF-related + various components of which some are African, because that is exactly what PPN is also.

I haven't seen any stats with Natufians for the ancient East Africans, but apparently Maasai and Somalis are equidistant between PPNB and Natufians. There's no Natufian in the qpAdm population set, so maybe something more toward Natufian than PPNB would fit. I'd like to see that stats for them and ancient Egyptians, and of course for IAM when the genomes are released.

The biggest outlier for Luxmanda is with South_Africa_2000BP though, possibly meaning Mota is too southern on the East-South Africa cline as a reference; maybe Luxmanda has a bunch of ancestral East African ancestry from further north?

Glad to see someone question this confusing part of the paper. The way I see it, Mota has a unique population history, distinct from any known SSA population. According to Llorente et al, Mota shares more drift with modern Maghrebis than with their Central African and southern African populations. Mota also shares more drift with highly admixed Ethio-Semitic speakers than with most Sub-Saharan Africans. AFAIK, no known SSA genome has such affinities, while simultaneously showing a lack of detectable Eurasian ancestry. So I'm surprised various authors don't question their data when it comes back saying that the SSA ancestry in Hadza, Luxmanda etc. is 100% derived from Mota. At best Mota is a provisional placeholder for their SSA-like ancestry, until better samples are found.

This opens up the possibility that some of Luxmanda's SSA ancestry has, as you suggest, a more northern origin. We can't say for sure, because the analyses describing her ancestry so far are not very sophisticated. But I would be surprised if this part of her ancestry derives as far north as the Lower Nile Valley.

quote:
Originally posted by capra:
From what I understand PPNB didn't really expand into Egypt, there's some influence - livestock obviously, Helwan-type points, but doesn't look like a wholesale migration really? But I may have picked that up from some unreliable source, like Afrocentrists. [Wink]

If (rock) art is anything to go by, there is a gradual lightening of the pigment used to paint skin in North African art. Skin pigmentation in pre-Neolithic times was darker, while Neolithic and predynastic skin pigmentation was lighter on average (e.g. an extreme example of lighter pigmentation used during the Neolithic and an example from the predynastic). In dynastic times it was more variable, including all of the above pigmentaton levels and even lighter forms of reddish not seen in earlier periods. So, we have a range of brown in the early Holocene, and progressively more reddish shades in mid-Holocene times, until we get to the distinctly ochre red pigments used in some later dynastic art.

Some Afroasiatic speakers still place themselves and their neighbours on a black-red spectrum, so it's tempting to see the gradual use of more reddish pigments as really reflecting an awareness of skin pigmentation in different time periods.

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Swenet
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quote:
Originally posted by Elmaestro:
Swenet makes a good point...
quote:
BTW, this is also why I'm very sceptical of claims that the non-SSA ancestry in Africa (e.g. Luxmanda) is actually PPN. It's anachronistic as it does not fit the aforementioned trend of homogenization. Luxmanda's so-called PPN could easily be something EEF-related + various components of which some are African, because that is exactly what PPN is also. I think when predynastics are sampled, their non-SSA ancestry will show a preference for PPN and Natufians (compared to EEF). But, taken literally, this is similarly bogus for all the aforementioned reasons.
I cosign the Model, but to me whatever falls inline with being EEF-like is simply NorthAfrican Ancestry shared between European Neolithic Groups... Which I believe is supported by the ruling out of Anatolian Admixture (Skoglund 2017).
IIRC, they just ruled out an Anatolian source—not an Anatolian contribution. It seems to me that, if Luxmanda's non-SSA part specifically resembles PPN, as the authors claim, then part of it would have to be Anatolian Neolithic.

quote:
Originally posted by Elmaestro:
the remainder of Luxmandas ancestry not shared with African groups in the paper is more related to the Near east (some if not all is actually due to admixture FMPOV)... regardless, this doesn't happen with a archetypal African Basal Eurasian subgroup existing, unless its North African... how does that Idea hold up with NAfrican aDNA, KEB can't be Basal Eurasian like, ...IAM, maybe, however, if you can prove introgression from Ibermaurasians and Model the remaining outgroup as both African but not SSAn... But once again, I don't know how well this is supported by archaeology

I don't understand what you mean here. But if you maintain that Basal Eurasian is Iranian or Arabian, then you can't say that the African ancestry in Luxmanda, IAM and KEB is underestimated. The biggest common denominator in the non-SSA ancestry of all these populations is Basal Eurasian. If you maintain that Basal Eurasian is not African, then you're essentially saying the same thing as Polako (i.e. that only the SSA-like ancestry in these populations is African).
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quote:
don't understand what you mean here. But if you maintain that Basal Eurasian is Iranian or Arabian, then you can't say that the African ancestry in Luxmanda, IAM and KEB is underestimated. The biggest common denominator in the non-SSA ancestry of all these populations is Basal Eurasian. If you maintain that Basal Eurasian is not African, then you're essentially saying the same thing as Polako (i.e. that only the SSA-like ancestry in these populations is African).
Not if I believe Lazaridis' basal Eurasian can't be a singlepopulation. If you recall I was open to the idea of a "pseudo basal Eurasian" expansion from North Africa but as far as the laz 2016 distribution goes, I don't see all those non african populations sharing the same African ancestry. How do you go about explaining shared ancestry between CHG (@ ~30%) and Ancient African for example?

And yeah they weren't particularly transparent on what they meant by Anatolian ancestry but I have a hard time believing they'd consider luxmanda as a possible source for such ancestry in PPNB... Why they didn't include natufians in qpAdm is another story/possible complaint.

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Swenet
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quote:
Originally posted by Elmaestro:
quote:
don't understand what you mean here. But if you maintain that Basal Eurasian is Iranian or Arabian, then you can't say that the African ancestry in Luxmanda, IAM and KEB is underestimated. The biggest common denominator in the non-SSA ancestry of all these populations is Basal Eurasian. If you maintain that Basal Eurasian is not African, then you're essentially saying the same thing as Polako (i.e. that only the SSA-like ancestry in these populations is African).
Not if I believe Lazaridis' basal Eurasian can't be a singlepopulation. If you recall I was open to the idea of a "pseudo basal Eurasian" expansion from North Africa but as far as the laz 2016 distribution goes, I don't see all those non african populations sharing the same African ancestry. How do you go about explaining shared ancestry between CHG (@ ~30%) and Ancient African for example?

And yeah they weren't particularly transparent on what they meant by Anatolian ancestry but I have a hard time believing they'd consider luxmanda as a possible source for such ancestry in PPNB... Why they didn't include natufians in qpAdm is another story/possible complaint.

What about CHG? CHG forms a clade with EEF to the exclusion of non-Basal Eurasian carriers (Jones et al 2015). That's unequivocal evidence as far as Basal Eurasian being a single ancestral population. If I'm understanding you right, you say it's a contradiction for CHG to have additional types of African ancestry (i.e. other than Basal Eurasian). What is the contradiction, in your view? The fact that additional types of African ancestry consistently accompany Basal Eurasian carriers is not exactly damning evidence against an African origin. Lol.

Placing Basal Eurasian in or outside of Africa would not solve your position that Basal Eurasian is not a single population. Meaning, if you think Basal Eurasian is not a single population in Africa, it'd be similarly odd for them to be a single population in Iran or Arabia. The question of what they are is a separate discussion from where they lived, except that their 'geographical extent' is constrained since they were tropically adapted. (I.e. they must have lived near the tropics). That is an example of a connection I see between their genetic make up and their homeland, that justifies placing them somewhere, over other places. But if your argument is that they weren't a single population, relegating them to Iran or Arabia merely displaces (not solve) the problem you see with an African origin.

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quote:

We have previously reported massive gene flow ~3,000 ya from Eurasians to Ethiopian populations.4 Here, we reassess the presence of Eurasian ancestry in Africa by using f3 statistics25 in the form of f3:X; Eurasian, Yoruba, where a negative value with a Z score < -4 indicates that X is a mixture of Africans and Eurasians. We found, as expected, that most Ethiopians are a mixture of Africans and Eurasians. An exception is the Gumuz population, where f3: Gumuz; Eurasian, Yoruba is always positive. The Gumuz language belongs to the Nilo-Saharan family, which could have isolated the Gumuz from the Afro-Asiatic-speaking Ethiopians. However, we found that the Toubou in Chad, who also speak a Nilo-Saharan language, are a mixture of Africans and Eurasians, making f3:Toubou; Eurasian, Yoruba always significantly negative. This suggests that the impact of Eurasian migrations today extends beyond East Africa and the Afro-Asiatic-speaking populations.

Whenever these monyockos include Afro-Asiatic-speaking populations it degenerates into nonsense.
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quote:
Originally posted by Swenet:
What about CHG? CHG forms a clade with EEF to the exclusion of non-Basal Eurasian carriers (Jones et al 2015). That's unequivocal evidence as far as Basal Eurasian being a single ancestral population. If I'm understanding you right, you say it's a contradiction for CHG to have additional types of African ancestry (i.e. other than Basal Eurasian). What is the contradiction, in your view? The fact that additional types of African ancestry consistently accompany Basal Eurasian carriers is not exactly damning evidence against an African origin. Lol.

Placing Basal Eurasian in or outside of Africa would not solve your position that Basal Eurasian is not a single population. Meaning, if you think Basal Eurasian is not a single population in Africa, it'd be similarly odd for them to be a single population in Iran or Arabia. The question of what they are is a separate discussion from where they lived, except that their 'geographical extent' is constrained since they were tropically adapted. (I.e. they must have lived near the tropics). That is an example of a connection I see between their genetic make up and their homeland, that justifies placing them somewhere, over other places. But if your argument is that they weren't a single population, relegating them to Iran or Arabia merely displaces (not solve) the problem you see with an African origin.

Iight, you got me there, I respect that...

Not trying to go too deep into Eurasian DNA, but I didn't know it's appropriate to equate EEF - CHG relatedness to shared admixture as opposed to shared ancestry. As it relates to the latter, how far back can you possibly push BE geneflow (as a singular population) to Eurasia and how relevant would they be if you do you so? I'm saying that relevant North African dispersal post-dates the split in EEF and CHG, & I don't think relatively recently shared African Ancestry is responsible for bringing EEF and CHG together.

My theory was that the closest thing that'd resemble Lazaridis' BE is a post Bottleneck/Homogenized Iranian/Arabian With limited admixture from other ancient Eurasian groups and no Archaic introgression... the kicker though is that though this populations Autosomal profile fits the description it isn't responsible for the "BasalEurasian" ancestry we find in all modern west Eurasian populations, however it's the default proximity towards Africans that would create these false positives. So in actually, that is why I suggest caution in putting Lazaridis' "Basal Eurasian" Eurasian in Africa, despite converting my beliefs on indigenous North Africa.

It's a safety net for shit like this, which is even stated in the OP as we speak.
quote:
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 admix- ture 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).Wefound that this model was consistent with the data (p = 0.53) (transition SNPs excluded to a final set of 110,507 trans- version 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).

-See Support for a single out-of-Africa founding population

..It'll better explain how Basal Eurasian is undetected as a secondary wave of migration, than a mass expansion of Africans >20kya, and it's consistent with the timing of Iranian Haplogroup dispersal in Europe, etc. This is why I had put so much emphasis of the differences among SSAfrican signals in Eurasians.
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Swenet
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quote:
Originally posted by Elmaestro:
quote:
Originally posted by Swenet:
What about CHG? CHG forms a clade with EEF to the exclusion of non-Basal Eurasian carriers (Jones et al 2015). That's unequivocal evidence as far as Basal Eurasian being a single ancestral population. If I'm understanding you right, you say it's a contradiction for CHG to have additional types of African ancestry (i.e. other than Basal Eurasian). What is the contradiction, in your view? The fact that additional types of African ancestry consistently accompany Basal Eurasian carriers is not exactly damning evidence against an African origin. Lol.

Placing Basal Eurasian in or outside of Africa would not solve your position that Basal Eurasian is not a single population. Meaning, if you think Basal Eurasian is not a single population in Africa, it'd be similarly odd for them to be a single population in Iran or Arabia. The question of what they are is a separate discussion from where they lived, except that their 'geographical extent' is constrained since they were tropically adapted. (I.e. they must have lived near the tropics). That is an example of a connection I see between their genetic make up and their homeland, that justifies placing them somewhere, over other places. But if your argument is that they weren't a single population, relegating them to Iran or Arabia merely displaces (not solve) the problem you see with an African origin.

Iight, you got me there, I respect that...

Not trying to go too deep into Eurasian DNA, but I didn't know it's appropriate to equate EEF - CHG relatedness to shared admixture as opposed to shared ancestry. As it relates to the latter, how far back can you possibly push BE geneflow (as a singular population) to Eurasia and how relevant would they be if you do you so? I'm saying that relevant North African dispersal post-dates the split in EEF and CHG, & I don't think relatively recently shared African Ancestry is responsible for bringing EEF and CHG together.

My theory was that the closest thing that'd resemble Lazaridis' BE is a post Bottleneck/Homogenized Iranian/Arabian With limited admixture from other ancient Eurasian groups and no Archaic introgression... the kicker though is that though this populations Autosomal profile fits the description it isn't responsible for the "BasalEurasian" ancestry we find in all modern west Eurasian populations, however it's the default proximity towards Africans that would create these false positives. So in actually, that is why I suggest caution in putting Lazaridis' "Basal Eurasian" Eurasian in Africa, despite converting my beliefs on indigenous North Africa.

It's a safety net for shit like this, which is even stated in the OP as we speak.
quote:
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 admix- ture 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).Wefound that this model was consistent with the data (p = 0.53) (transition SNPs excluded to a final set of 110,507 trans- version 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).

-See Support for a single out-of-Africa founding population

..It'll better explain how Basal Eurasian is undetected as a secondary wave of migration, than a mass expansion of Africans >20kya, and it's consistent with the timing of Iranian Haplogroup dispersal in Europe, etc. This is why I had put so much emphasis of the differences among SSAfrican signals in Eurasians.

When you leave Basal Eurasian (BE) out of the picture, and look at the non-BE ancestry in EEF and CHG, EEF will be related to WHG and what remains of CHG will be related to Russian HGs). As soon as you allow Basal Eurasian back into the picture, EEF and CHG start to form a clade. This is incongruent, because they are most closely related to WHG and Russian HGs, respectively. The only explanation of this is that BE is drawing these otherwise distant populations together.

My money is on Basal Eurasian being mostly a result of postglacial movements out of northeast Africa and spreading in all directions (including the Maghreb, the Sinai, the Aegean and other coasts to the west). There might have been older, pre-existing pockets of groups with Basal Eurasian in the Middle East, but most Middle Eastern ancestry will fit somewhere on this ancient DNA landscape, which so far has been a complete Basal Eurasian desert before 14kya. I see that Sub-Saharan ancestry which you take as an argument against Basal Eurasian, as ancestry that Basal Eurasians mixed with right before migrating to the Middle East:

quote:
From the African BSP (Figure 3B), all the African random samples also showed a 5-fold growth at ~15−11 kya, corresponding to expansion haplogroups L0a1a, L1b1a, L1b1a3, L2a1a, L3b1a, L3e1, L3e2a and L3e2b, and subsequently a 2-fold growth ~5−4kya, which might be driven by the Neolithic Revolution.
https://www.nature.com/articles/srep00745

^Hence, the ~5% West/Central African ancestry in the recently sampled Natufians. I also expect the maximum percent of SSA ancestry, as well as the maximum amount of Basal Eurasian, to increase as samples of these new arrivals get closer to the 14ky date and as more endogamous members among these new arrivals are sampled. For instance, the Natufians found in the Shuqbah cave are good examples of more endogamous arrivals in the Levant, in my view. I expect the same for all other Neolithic regions with notable Basal Eurasian.

Those are some of my predictions for future aDNA. Feel free to hold me to every single point.

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the lioness,
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 -


 -
Oase 2


DNA analysis of Oase 1 since 2015 has made a number of significant findings.

About 6%-9% of the genome is Neanderthal in origin. This is the highest percentage of archaic introgression found in an anatomically modern human and suggests that Oase 1 had a relatively-recent Neanderthal ancestor – about four to six generations earlier.

The autosomal DNA of Oase 1 by Fu et al. (2015) indicates that he may have shared more alleles with modern East Asian populations than with modern Europeans. However Oase shared equal alleles with Mesolithic Europeans and East Eurasians suggesting non-European admixture in modern Europeans[7]
Oase 1 belongs to an extinct Y-DNA haplogroup and an extinct mitochondrial DNA haplogroup.
Research by Poznik et al. (2016) suggests that Oase 1 belongs to haplogroup K2a*. That is, Oase 1 possesses SNPS similar to Ust'-Ishim man (also K2a*), 45,000-year-old remains from Siberia, and upstream from a rare lineage found in two living males (from ethnic Telugu and Malay backgrounds, respectively, for whom Poznik et al. proposed the creation of a new subclade, named "K2a1").[8] (Earlier research by Fu et al. reported that Oase 1 belonged to a subclade of Y-DNA haplogroup F, other than haplogroups G, H, I and J – leaving open the possibility that Oase 1 belonged to macrohaplogroup K.)
According to Fu, Oase-1 belongs to a basal subclade of mitochondrial DNA haplogroup N.[7] (General research into N* has found that it occurs at its highest frequencies among the modern populations of Socotra,[9] and Somalia, albeit only at levels of 20–24%.[10] It is also found at low frequencies among Algerians and Reguibate Sahrawi.[

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capra
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Oase I is a basal Eurasian but not the Basal Eurasian. His N is not even true N* but pre-N, which is (as far as anyone knows) long extinct. So there is no reason to connect it to modern N*; for that matter one N* is no more relatable to any other N* that it is to an identified N branch.
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Elite Diasporan
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This point right here makes sense imo.
quote:
My money is on Basal Eurasian being mostly a result of postglacial movements out of northeast Africa and spreading in all directions (including the Maghreb, the Sinai, the Aegean and other coasts to the west). There might have been older, pre-existing pockets of groups with Basal Eurasian in the Middle East, but most Middle Eastern ancestry will fit somewhere on this ancient DNA landscape, which so far has been a complete Basal Eurasian desert before 14kya. I see that Sub-Saharan ancestry which you take as an argument against Basal Eurasian, as ancestry that Basal Eurasians mixed with right before migrating to the Middle East:

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Swenet
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quote:
Originally posted by Elite Diasporan:
This point right here makes sense imo.

Postglacial times are filled with special dates in African population history (e.g. the TMRCA of modern Afroasiatic, Niger-Kordofanian and Y DNA mutations, like E-M2, E-M81 and E-M78 which would later replace most Sub-Saharan and North African Y lineages). Indications of dramatic postglacial demographic events and population growth make Africa, by far, best positioned to be the source of Basal Eurasian.

There is no evidence that non-African homelands often suggested for Basal Eurasian could have supported a population large enough to fundamentally change the entire Middle East. At least Africa has several precedents of having done exactly that in ancient times. Ancestral Semitic speakers being the most recent example.

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


DNA analysis of Oase 1 since 2015 has made a number of significant findings.

About 6%-9% of the genome is Neanderthal in origin. This is the highest percentage of archaic introgression found in an anatomically modern human and suggests that Oase 1 had a relatively-recent Neanderthal ancestor – about four to six generations earlier.

The autosomal DNA of Oase 1 by Fu et al. (2015) indicates that he may have shared more alleles with modern East Asian populations than with modern Europeans. However Oase shared equal alleles with Mesolithic Europeans and East Eurasians suggesting non-European admixture in modern Europeans[7]
Oase 1 belongs to an extinct Y-DNA haplogroup and an extinct mitochondrial DNA haplogroup.
Research by Poznik et al. (2016) suggests that Oase 1 belongs to haplogroup K2a*. That is, Oase 1 possesses SNPS similar to Ust'-Ishim man (also K2a*), 45,000-year-old remains from Siberia, and upstream from a rare lineage found in two living males (from ethnic Telugu and Malay backgrounds, respectively, for whom Poznik et al. proposed the creation of a new subclade, named "K2a1").[8] (Earlier research by Fu et al. reported that Oase 1 belonged to a subclade of Y-DNA haplogroup F, other than haplogroups G, H, I and J – leaving open the possibility that Oase 1 belonged to macrohaplogroup K.)
According to Fu, Oase-1 belongs to a basal subclade of mitochondrial DNA haplogroup N.[7] (General research into N* has found that it occurs at its highest frequencies among the modern populations of Socotra,[9] and Somalia, albeit only at levels of 20–24%.[10] It is also found at low frequencies among Algerians and Reguibate Sahrawi.[ [/QB]

quote:
Originally posted by capra:
Oase I is a basal Eurasian but not the Basal Eurasian. His N is not even true N* but pre-N, which is (as far as anyone knows) long extinct. So there is no reason to connect it to modern N*; for that matter one N* is no more relatable to any other N* that it is to an identified N branch.

What is this "pre haplogroup" you speak of?

N* is the basal N. That is pre N and it's found in modern populations as quoted above.
Oase is 30-45 kya

Didn't you mention Ust'-Ishim earlier?
What about K2a*

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Elite Diasporan
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@Swenet

Again very good point. When we always discuss genetic history of a region of the world we always forget to add the context of the environment/climate of that time. Sure we bring up the Sahara(desert vs fertile) but we never talk about the other climate events.


Even when the ice sheets were retreating Southern Europe and Northern Southwest Asia would have still been quite cold for a large population. Africa would have easily been able to support a large population that would have been ancestral to basel Eurasian.

I mean not to go off-topic but I feel this is a good example. Look at the population of Canada. Only 30,000,000 million people. The African-American population is larger than that. But why is that?

Sure Southern Canada is densely populated and not in the arctic.
 -

But the majority of Canada IS in the arctic. And while Canada is much bigger than the USA. The USA can more easily support a larger and diverse population. To me this would have been the same with Africa vs Western Eurasia.

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the lioness,
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Isn't basal Eurasian of topic? I thought the topic is Neolithic, much more recent
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Swenet, I've read a few studies indicating ANE influence in prehistoric SW Asia and such influence would seem to correlate with hg R lineages in that region. If so, do you identify ANE as being a possible component in EEF and thus its arrival in Africa?
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Elmaestro
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@Elite Diasporan
You have to be aware that that particular point you're elaborating on can also be a counter argument. Lazaridis' Basal Eurasian should be some what homogenized suggesting founder, or drift. A large founding population increases the gene pool and so far we are collectively doing a poor job of detecting ancient recombination with modern and some ancient African populations.

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Djehuti
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quote:
Originally posted by the lioness,:
http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23285/full

Internal diversification of non-Sub-Saharan haplogroups in Sahelian populations and the spread of pastoralism beyond the Sahara july 2017


Authors
Iva Kulichová,
Verónica Fernandes,
Alioune Deme,
Jana Nováčková,
Vlastimil Stenzl,
Andrea Novelletto,
Luísa Pereira,
Viktor Černý


Abstract

Background

Today, African pastoralists are found mainly in the Sahel/Savannah belt spanning 6,000 km from west to east, flanked by the Sahara to the north and tropical rainforests to the south. The most significant group among them are the Fulani who not only keep cattle breeds of possible West Eurasian ancestry, but form themselves a gene pool containing some paternally and maternally-transmitted West Eurasian haplogroups.
Materials and Methods

We generated complete sequences for 33 mitogenomes belonging to haplogroups H1 and U5 (23 and 10, respectively), and genotyped 16 STRs in 65 Y chromosomes belonging to haplogroup R1b-V88.
Results

We show that age estimates of the maternal lineage H1cb1, occurring almost exclusively in the Fulani, point to the time when the first cattle herders settled the Sahel/Savannah belt. Similar age estimates were obtained for paternal lineage R1b-V88, which occurs today in the Fulani but also in other, mostly pastoral populations. Maternal clade U5b1b1b, reported earlier in the Berbers, shows a shallower age, suggesting another possibly independent input into the Sahelian pastoralist gene pool.
Conclusions

Despite the fact that animal domestication originated in the Near East ∼ 10 ka, and that it was from there that animals such as sheep, goats as well as cattle were introduced into Northeast Africa soon thereafter, contemporary cattle keepers in the Sahel/Savannah belt show uniparental genetic affinities that suggest the possibility of an ancient contact with an additional ancestral population of western Mediterranean ancestry.

I take it you already forgot about the dozens of past threads on the topic where we told you the 'Fulani' are a large cultural group comprised of many tribes and that some in the Western Sahel display typical West African NRY hg E1b1a at 100% while others in the Eastern Sahel in Sudan and near the Horn display hg T like some Horn populations. Therefore the conclusions of this paper may only apply to a subgroup of Fulani but not the entire cultural group.

Lastly what does this have to do with ancient Tanzanian Pastoralists??

--------------------
Mahirap gisingin ang nagtutulog-tulugan.

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Elite Diasporan
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quote:
Originally posted by Elmaestro:
@Elite Diasporan
You have to be aware that that particular point you're elaborating on can also be a counter argument. Lazaridis' Basal Eurasian should be some what homogenized suggesting founder, or drift. A large founding population increases the gene pool and so far we are collectively doing a poor job of detecting ancient recombination with modern and some ancient African populations.

Noted.
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capra
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Sorry to go further off topic, but paragroups seem to cause a lot of confusion

quote:
Originally posted by the lioness,:
What is this "pre haplogroup" you speak of?
N* is the basal N. That is pre N and it's found in modern populations as quoted above.

Pre-haplogroup is an informal way of referring to a lineage with some, but not all, of the mutations defining that haplogroup. If you look at PhyloTree you can see there are 5 mutations shared by N. Oase-1 is missing two of them: he has ancestral 8701G and 9540C. Likewise MA-1 is missing some of the mutations leading to Y haplogroup R, so we can call him pre-R. This is just to avoid reorganizing the entire frigging tree to account for a single extinct ancient lineage.

Pre-N is not the same as N*, which is anything that belongs to haplogroup N but not to any known branch that could be detected by the study in question. N* just means "unidentified branch of N". In fact unless it is a full sequence it is probably part of some known branch. All known full N sequences other than Oase-1 have all 5 mutations and hence are N and not pre-N. So an N* branch is parallel to identified N branches, it doesn't branch off before them, it is not basal or earlier.

All three of the sources cited in the Oase-1 Wikipedia article sequenced only the HVS-1 and few coding region mutations, which is a lot cheaper than full sequencing but can make it impossible to determine the actual haplogroup. Now, the second source cited by Wikipedia decided that the N* from Soqotra reported in the first source was actually either I3 or I5. However, the Wikipedia editor who put this stuff in ignores that and refers to all of it as N* anyway. [Roll Eyes] In fact this Soqotri N* is I5a according to Fernandes et al 2012, I5a2a on PhyloTree. The Algerian N from the third source is some other random subclade unrelated to the Yemeni one.

None of it has anything to do with Oase-1. Oase-1 is not any more closely related to any modern N* than he is to, say, U6a1a, or W3b2, or anything else under haplogroup N. You should know better than to trust random junk on Wikipedia, Lioness.

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