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Author Topic: Ancient Tanzanian Pastoralist results... VERY interesting stuff!
the lioness,
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It's not random junk. It's all referenced in scientific articles

http://www.nature.com/nature/journal/v524/n7564/full/nature14558.html?foxtrotcallback=true

An early modern human from Romania with a recent Neanderthal ancestor

David Reich, Svante Pääbo et al

Nature 524, 216–219 (13 August 2015) doi:10.1038/nature14558
2015
_________________________________

If basal Eurasian remains were found
-How would they know they were basal Eurasian?


However I'm not going to pursue it further because basal Eurasian is off topic. The topic is

•Genome-wide analysis of 16 African individuals who lived up to 8,100 years ago

But "Basal Eurasian" is tens of thousands of years later


quote:

Basal Eurasian and Neanderthal ancestry
The ‘Basal Eurasians’ are a lineage hypothesized13 to have split off before the differentiation of all other Eurasian lineages, including eastern non-African populations such as the Han Chinese, and even the early diverged lineage represented by the genome sequence of the ~45,000-year-old Upper Palaeolithic Siberian from Ust’-Ishim11


The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans ~50,000–60,000 years ago11 largely occurred after the splitting of the Basal Eurasians from other non-Africans.

The idea of Natufians as a vector for the movement of Basal Eurasian ancestry into the Near East is also not supported by our data, as the Basal Eurasian ancestry in the Natufians (44 ± 8%) is consistent with stemming from the same population as that in the Neolithic and Mesolithic populations of Iran, and is not greater than in those populations

--Genomic insights into the origin of farming in the ancient Near East
Iosif Lazaridis

I don't know why the basal eurasian hypothetic keeps getting brought up in Neolithic studies, it's Lazaridis fault
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the lioness,
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quote:
Originally posted by Djehuti:


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

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?


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


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

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? .....

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.




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the lioness,
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It's not random junk. It's all referenced in scientific articles

http://www.nature.com/nature/journal/v524/n7564/full/nature14558.html?foxtrotcallback=true

An early modern human from Romania with a recent Neanderthal ancestor

David Reich, Svante Pääbo et al

Nature 524, 216–219 (13 August 2015) doi:10.1038/nature14558
2015
_________________________________

If basal Eurasian remains were found
-How would they know they were basal Eurasian?


However I'm not going to pursue it further because basal Eurasian is off topic. The topic is

•Genome-wide analysis of 16 African individuals who lived up to 8,100 years ago

But "Basal Eurasian" is tens of thousands of years earlier


quote:

Basal Eurasian and Neanderthal ancestry
The ‘Basal Eurasians’ are a lineage hypothesized13 to have split off before the differentiation of all other Eurasian lineages, including eastern non-African populations such as the Han Chinese, and even the early diverged lineage represented by the genome sequence of the ~45,000-year-old Upper Palaeolithic Siberian from Ust’-Ishim11


The finding of little if any Neanderthal ancestry in Basal Eurasians could be explained if the Neanderthal admixture into modern humans ~50,000–60,000 years ago11 largely occurred after the splitting of the Basal Eurasians from other non-Africans.

The idea of Natufians as a vector for the movement of Basal Eurasian ancestry into the Near East is also not supported by our data, as the Basal Eurasian ancestry in the Natufians (44 ± 8%) is consistent with stemming from the same population as that in the Neolithic and Mesolithic populations of Iran, and is not greater than in those populations

--Genomic insights into the origin of farming in the ancient Near East
Iosif Lazaridis

I don't know why the basal eurasian hypothetic keeps getting brought up in Neolithic studies, it's Lazaridis fault
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Swenet
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quote:
Originally posted by Elite Diasporan:
@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.

People do this all the time. They make elaborate narratives with no regard for things that hamper or promote growth and migration. One of the reasons I saw through that claim on ABF about Malawian-mediated Neolithization of South Africa is because Malawi is in the middle of Tsetse-infested zone.
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Swenet
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quote:
Originally posted by Djehuti:
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?

I can't prove it as I've never looked for admixture analyses, but I think so, yes. The R-V88(?)-carrying farmer in Spain (el Trocs [see Haak et al 2015]) seems indistinguishable from non-R1b-carrying EEF. But ANE-related ancestry is probably still in his genome. Just like L3b-related African ancestry in the Russian below is still present at low levels that most tools used by hobbyists probably wouldn't pick up on.

quote:

Table 4 shows the comparison of the frequencies of
alleles of the autosomal microsatellite loci found in
Russians with mitochondrial haplotypes of African
origin in European, African, and Russian populations.
We found that the autosomal haplotypes of the Rus-
sians carrying African mtDNA haplotypes were
mainly characterized by alleles common to European
and African populations. However, Russians had alle-
les that are characteristic of Europeans but are
extremely rare in Africans (e.g., D13S317*8,
D13S17*9, D81179*10, and D19S433*15 in an L1b
subject and D18S51*17 in an L3b subject), which
indicates their European origin. Only two alleles
found in an L3b Russian subject (D2S1338*22 and
TPOX*7) were frequent in Africans but extremely rare
or absent in Russians. Apparently, these alleles are a
genetic trace of a past mixing of races.


https://www.ncbi.nlm.nih.gov/pubmed/16240714

Other R1b carrying European farmers might have much more ANE than Troc3, though. I just mentioned him because I'm more familiar with him than with other European R carrying farmers that have been found more recently.

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Elite Diasporan
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Wow... lol. I see "lol_race" didn't read this study. Him and others still pushing the idea that this women wasnpurely South Cushite.

quote:
Originally posted by Swenet:
People do this all the time. They make elaborate narratives with no regard for things that hamper or promote growth and migration. One of the reasons I saw through that claim on ABF about Malawian-mediated Neolithization of South Africa is because Malawi is in the middle of Tsetse-infested zone.

lol. I remember that Malawian discussion. But yeah people usually forget the context of certain environmental issues.
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Swenet
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Lol at the results posted in that thread in light of my comments on EEF-related ancestry in Luxmanda. Good to know my aDNA radar is on point.
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Elmaestro
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The non African signatures were probably partially allocated to "East African pastoralists" and the less "med farmer" is shared with Europeans the higher luxmanda should score for it, I expect higher proportion of North African*.
..But then again, it's just GEDmatch

Near East Neolithic K13 Oracle results:

gedrosia K13 Oracle

code:
1	SUB_SAHARAN	        50.15
2 NATUFIAN 30.41
3 ANATOLIA_NEOLITHIC 11.04
4 IRAN_NEOLITHIC 1.51
5 EHG 1.43
6 SHG_WHG 1.41
7 SIBERIAN 1.36
8 PAPUAN 1.33
9 SE_ASIAN 1.23
10 ANCESTRAL_INDIAN 0.12

Now 12-13% of luxmandas SSAn is elsewhere

code:
#	 	Primary Population (source)	Secondary Population (source)	Distance
1 66.1% Hadza + 33.9% Levant_N @ 5.39
2 64.3% Hadza + 35.7% Levant_BA @ 5.62
3 74.9% Masai + 25.1% Levant_N @ 5.91
4 61.8% Mota + 38.2% Levant_BA @ 6.78
5 63.6% Mota + 36.4% Levant_N @ 6.89
6 73.6% Masai + 26.4% Levant_BA @ 7.09
7 51.5% Gambian + 48.5% Levant_BA @ 7.95
8 50.1% Levant_BA+ 49.9% Esan @ 8.16
9 50.1% Levant_BA+ 49.9% Yoruba @ 8.16
10 60.1% Masai + 39.9% Moroccan @ 8.21
11 66.2% Masai + 33.8% Libyan @ 8.73
12 61.2% Masai + 38.8% Saharawi @ 8.74
13 50.2% Hadza + 49.8% Saharawi @ 8.75
14 72.8% Masai + 27.2% Jew_Libyan @ 9.19
15 67.9% Masai + 32.1% Egyptian @ 9.3
16 55.6% Hadza + 44.4% Libyan @ 9.3
17 77.9% Masai + 22.1% Anatolia_ChL @ 9.31
18 73.3% Masai + 26.7% Jew_Tunisian @ 9.37
19 52.8% Saharawi+ 47.2% Mota @ 9.47
20 63.5% Masai + 36.5% Algerian @ 9.48


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Elite Diasporan
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@Djehuti

I need to send you a PM if you are still around.

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Elmaestro
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Was in a fairly decent mood, decided to killed some free time, inspired by Capra and BBH, I decided to Run Some DStats. It is very telling as it pretty much clears up most if not all of the questions surrounding Luxmandas Non-SubSaharan Ancestry... so maybe my time wasn't all that wasted. Blue text denotes best fit and Z-score, Red text is worst Stat, blue bg is the best Z-Score.

Quick breakdown: It appears that Luxmandas NonSSA might be an intermediate between Natufians and PPNB (more shifted towards PPNB), EEF-Anatolian like ancestry in Luxmanda is amplified by relatively non-Admixed Africans. However, when looking at Modern admixed populations; Cushitic, Nubian, we see signs of Anatolian Admixture dropping due to these newer population having more recent Anatolian-like ancestry (Nubians, Beja) or similar ancestry being wide spread in the source populations for non African Admixture (Somali).
..thoughts, anyone?

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capra
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Thanks for these, Elmaestro.

A little tricky with these indirect comparisons but I think I see what you are saying. The Beni Amer and Halfawieen have a little more affinity to Anatolian than to Levant_N while the opposite is the case with Luxmanda, so the former have not only more but slightly different composition of the MENA portion of their ancestry.

With Luxmanda, Somali; WA, Mbuti the difference between the ancient West Asian references is negligible, so Somalis seem to have much the same amount and composition of MENA as Luxmanda.

But in the paper Somalis were modelled as 16% Iran_N, 22% Dinka, 62% Luxmanda - that would make 40% of their MENA ancestry Iran_N. No way that should work! Are these different Somali populations being tested?

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Elite Diasporan
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^Wait so Somalis are only 30% MENA?
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capra
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Luxmanda was modelled as about 38% PPNB (36-39% range). By Elmaestro's stats Somalis should be about the same as Luxmanda.

Or, Somalis modelled in this study as 62% Luxmanda, 16% Iran_N, 22% Dinka. So 62% x 38% (of MENA in Luxmanda) = 24%, plus 16% for Iran_N comes to 40% MENA in total. All give or take a few percent.

Pickrell et al estimated Somalis at 38% MENA back in 2013, so this actually matches the previously accepted numbers very well.

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Elmaestro
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^You're right on the money.

To my knowledge the Somali samples are all uniform. They have a lil more MENA than Luxmanda, however they also have low amount of Mbuti-like ancestry possibly from bantu influences. I ran the same results with the chimp earlier and got negative Z-scores for Lux,Som;WA,Mbuti... So I can believe that their amounts of MENA is very close maybe a lil less than 40% as you say. However I don't think the differences among WAsian influences should be taken lightly, and the shared ancestry between those guys should also be respected.

for instance: Somalis are simultaneously more Modern SSAn(dinka-WAfr) and West-Eurasian than Luxmanda, the biggest differences in their non African ancestry is that of Iran_N, so if you fit Somali between Luxmanda,Dinka,Iran_N in qpAdm the Iranian component will have to compensate for the added SSan(dinka) ancestry. It's a bit convoluted but what's thought provoking is the possibility that Luxmanda might harbor shared ancestry between these West Asian groups, whether it is BE, N.African or whatever.. if that is true, how would we go about distinguishing which population mixed with Luxmanda and to what magnitude??

The more I look into it, the more I get suspicious about Skoglunds postulation in regards to Luxmanda being partially ancestral to PPNB... we might need to take it more seriously.

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beyoku
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quote:
Originally posted by Elmaestro:


The more I look into it, the more I get suspicious about Skoglunds postulation in regards to Luxmanda being partially ancestral to PPNB... we might need to take it more seriously.

IMO this is where all roads have been leading for while. I think the community at large is reluctant to make that jump due to long held biases....BUT it’s exactly what we would expect.

Speaking of “taking things more seriously”.....I think we are going to have to start taking some of those splits times and divergences a bit more literal a la XYYMAN style. When it comes to all his bio-anthro many of us have a different research styles and come from a different backgrounds. For better or for worse I think the newer group of folks looking into this have come to totally different conclusions than some of us “old guard” folks. There are plenty of scenarios I wouldn’t have even considered until someone with younger eyes took a look at the data and evaluated it. Ma’alta boy at 25kya has Amerindian affinities. The new skeleton out of East Asia at 40 kya has Amerindian affinities.

It’s pretty much “game over man”.

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capra
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quote:
Originally posted by Elmaestro:
The more I look into it, the more I get suspicious about Skoglunds postulation in regards to Luxmanda being partially ancestral to PPNB... we might need to take it more seriously.

yeah, I wonder if they were just being logically complete, or do they have some hunch or new model?

I don't like pure Basal Eurasian for it, not as worked out by Laziridis et al at least; didn't fit for East Africans before and doesn't fit for Luxmanda now. Some earlier population shared between West Asia and North Africa yes, the question is always why does Anatolia Neolithic work relatively well and why isn't Natufian the best fit?

But maybe there is a widely shared base Paleo-MENA population here, and there is not only the recognizable additional ancestry in Anatolians (WHG etc) pulling them away from it, but some unrecognized ghost contributing to Natufians which is pulling them away in a different direction?

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