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Friday, March 31, 2017

SAA 2017 tweets


I can't stand Twitter, but here are some interesting tweets from the Society for American Archeology (SAA) 2017 annual meeting courtesy of Alexander M. Kim aka. Sarkoboros:

- Late Neolithic/Bronze Age Baikal hunter-gatherers have EHG or MA1-like admixture, event not yet dated (link)


- Baikal hunter-gatherers at extreme of East Eurasian variation (link)


- [Ancient Egyptians] cluster w. Neol & Br Age Levant. STRUCTURE: important Natufian component, some Anatolian, Iran Neol (link)

- substantial mtDNA continuity from pre-Ptolemaic to Ptolemaic, L increased post-Roman (link)

- ancient Egyptians basically lack SSA affinity beyond other Eurasians until Roman times (link)



- several authors offered to withdraw from [Haak et al. 2015] paper when "Indo-European" used in title. all ultimately convinced to stay on (link)

- Corded Ware "more mobile than anything before or after" in Europe (link)

See also...

Ancient Egyptians less Sub-Saharan than modern-day Egyptians

108 comments:

Romulus said...

That's an interesting slide. Wonder what the dotted line separating Funnel Beaker Culture from other European Neolithic cultures means. What paper is it from?

Arza said...

Corded Ware "more mobile than anything before or after" in Europe

At the bottom of the slide:

"based on data from Kujawia, Poland"

Nice.

Arza said...

Additional thought:

no one before and after was as mobile, as CWC
at the same time PIE was brought and spread by highly mobile pastoralists

Game over?

Romulus said...

so funnel beaker is directly ancestral to cwc and the yamna are irrelevant? cool beans

Arza said...

From the slide:

Linear Pottery Culture
Very stable settlements
Little social hierarchy



LDG



Globular Amphora Culture
Less stable settlements
More hierarchy

••••••••••••••••••••••••

Linear Pottery Culture
Very stable settlements
Little social hierarchy



Funnel Beaker Culture



Corded Ware Culture
High mobility
Increasing social hierarchy



Bell Beaker
Less mobility
More hierarchy



EBA


There are also lines indicating the chronology, but dates are unreadable.

Rob said...

That Corded Ware slide is from a paper years ago. It's based on archaeology only and doesn;t imply conclusions about filiation.
It probably needs modification because Corded Ware settlements have since been found, and their economy isn't solely pastoral, but mixed- including agriculture and hunting.

Davidski said...

@Romulus

so funnel beaker is directly ancestral to cwc and the yamna are irrelevant? cool beans

Sure, why not, except for the fact that early Corded Ware is identical to Yamnaya and nothing like Funnel Beaker.

Romulus said...

That's because CWC = Funnelbeaker + genetically Yamnaya like HGs who had been in Eastern Europe and the Baltic for a long time before the Yamnaya existed.

Davidski said...

@Romulus

That's because CWC = Funnelbeaker + genetically Yamnaya like HGs who had been in Eastern Europe and the Baltic for a long time before the Yamnaya existed.

Sure, why not, except for the fact that early Corded Ware is nothing like a mixture of Funnel Beaker and Eastern European/Baltic foragers.

John Smith said...

Maybe Corded Ware is genetically Yamna like HGs who have been in Eastern Europe and the Baltic long before the Yamna existed without the funnelbeaker?

Davidski said...

@John Smith

Maybe Corded Ware is genetically Yamna like HGs who have been in Eastern Europe and the Baltic long before the Yamna existed without the funnelbeaker?

None of the foragers from Estonia, Latvia, Lithuania or Russia from the last three Baltic papers resembled Yamnaya or Corded Ware.

So which genetically Yamna like HGs are you talking about exactly?

John Smith said...

Maybe they are from Yamna. I was thinking the Mesolithic Ukrainian with R1a has he been studied?

Davidski said...

You mean the Neolithic Ukrainian with R1a. Ukraine_N on this plot.

http://eurogenes.blogspot.com.au/2017/02/first-look-at-baltic-and-ukrainian.html

Samuel Andrews said...

Maybe ancient Egyptains were basically like Bronze age_Jordan and the Middle Eastern guy found in Roman Britain.

Nirjhar007 said...

''several authors offered to withdraw from [Haak et al. 2015] paper when "Indo-European" used in title. all ultimately convinced to stay on ''

I find that hard to believe. There is nothing convincing about it .

Davidski said...

It never ceases to amaze me how common it is for people to reject the most obvious outcome simply because they had high hopes for a different outcome.

Some resistance resulting from disappointment is to be expected, but making a complete fool of yourself in the face of overwhelming evidence is just pathological.

Despite all the papers and data from the last few years showing Corded Ware to be genetic twins with Yamnaya, and obviously a migrant population from the steppe, I still need to point out the obvious here that Corded Ware can only be derived from Yamnaya or a very closely related steppe group, rather than, say, Funnel Beaker and/or Baltic foragers.

Funnel Beaker and/or Baltic foragers aren't even in the ballpark as ancestors of Corded Ware. What is even the point of claiming such a thing?

Aram said...

Funnelbeaker has probably something to do with R1b L51 moving to West Europe from East Europe via their territory and admixing with them.

Gihanga Rwanda said...

These samples appear to be from Abusir, which is just outside of Cairo, so definitely not "Middle Egypt." Anyway, if these ancient samples lack the ~15% East African ancestry present in both contemporary Copts and Egyptian Muslims, which can't be attributed to the slave trade, I wonder if these ancient individuals descended in large part from the Hyksos, a Semitic population who settled in the eastern Delta sometime before 1650 BC? I guess only more comprehensive sampling will solve this riddle.

Davidski said...

Seems rather unlikely that the first study looking at ancient Egyptians would be based on a population with any real chance of being largely of Hyksos origin.

rozenfag said...

@ Gihanga Rwanda : Abusir may mean Abusir el-Melek, which is close to Fayum.

Gihanga Rwanda said...

I am honestly surprised, but how else can we explain the comparable levels of East African ancestry (~15%) found in both Copts and Egyptian Muslims? This can't be attributed to the Arab slave trade (i.e. ~5% West-Central African ancestry in Muslims) and last I checked the Kushites didn't overrun Egypt during the Roman era.

Salden said...

>I am honestly surprised, but how else can we explain the comparable levels of East African ancestry (~15%) found in both Copts and Egyptian Muslims?

Answer: They samples are Ancient Lower Egyptians. Lower Egypt has long been more Levantine than Upper Egypt.

Davidski said...

Even if these samples are from near Cairo, the really interesting thing is that it looks like they have only minimal recent Sub-Saharan ancestry. Or maybe none at all.

So if there's significant Sub-Saharan ancestry in Upper Egypt at around the same time or earlier, then what, different Egyptian populations didn't have any contact with each other? I doubt it.

Seems like there won't be much Sub-Saharan ancestry in Upper Egypt either.

Gihanga Rwanda said...

I doubt it. We know that some ancient Egyptians had significant SSA ancestry, given the results of the Amarna mummies from Upper Egypt; DNAtribes used PopAffiliator and STRUCTURE with CODIS markers, which isn't a sufficient way to estimate exact admixture proportions, but is enough to place samples in "continental" groups. Correct?

Davidski said...

I have no idea how reliable limited STR marker panels are for ancient samples as old as these Egyptians?

Gihanga Rwanda said...

Most of the modern-day Egyptian samples that we have on file are Lower Egyptian from cities like Alexandria and various locales throughout the Delta. The few samples that I've seen from Upper Egypt proper, Aswan-Luxor, are significantly more East African.

Aram said...

African admizture in Egypt and Levant is not only slave's legacy.

They were other events also.

----

While the ethnic-based army was generally successful on the battlefield, it began to have negative effects on Fatimid internal politics. Traditionally the Berber element of the army had the strongest sway over political affairs, but as the Turkish element grew more powerful, it began to challenge this, and by 1020 serious riots had begun to break out among the Black African troops who were fighting back against a Berber-Turk Alliance.

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

Salden said...

The DNAtribes study isn't acceptable. See here:

http://s1.zetaboards.com/anthroscape/single/?p=3089128&t=8064231

Matt said...

Nice to see some numbers on the ancient Egyptians. Looks like I was wrong and misread too much into the abstracts as suggesting some SSA ancestry in Egyptians as showing some low level (5-10%).

Eurogenes K13 / Dienekes Globe13 (should be fairly sufficient for this purpose) go between 17% - 26% for their Egyptian subsamples, so 20% does imply SSA essentially absent in these ancient Egyptians (unless they calculate fairly different estimates for moderns). Also presumably this is back up by what Kim has discussed with the authors that isn't in the slide...

The f3 stats Alex Kim links are pretty blurry, but strong suggestion of shared drift with Levant N, Anatolia N and Europe EN (more so than with recent people?).

Re; clustering with N and BA Levant, upcoming paper on CA Levant might be one to watch for this as well:

http://sohp.fas.harvard.edu/files/shp/files/young_investigator_symposium_abstracts_10.29.16.pdf - "Ancient Genomics of the Levant Chalcolithic - The ancient Levant has experienced dramatic changes in population structure since the development of agriculture. Prior to and during the early Neolithic, the Levant was inhabited by populations that were highly differentiated from the rest of the Near East. By the Bronze Age, this high level of genetic differentiation had decreased dramatically, with an influx of Iran-like ancestry observed in Levantine populations.

However, little is known about genetic changes in this region in the ~4,000-year interval between the Neolithic and Bronze Age periods. This study reports on genome-wide ancient DNA collected from 23 individuals from the Chalcolithic period in the Levant. This dataset approximately doubles the amount of genome-wide ancient human DNA available from the Levant. Preliminary results suggest that the Levant Chalcolithic population possessed ancestry derived from Levant Neolithic (58.2%), Iran Chalcolithic (17.0%), and Anatolia Neolithic (24.8%) populations.
Additionally, analysis of Levant Bronze Age populations suggest that this Levant Chalcolithic population may represent a genetic dead end that did not contribute broadly to later groups."


(hard to tell if the broad ancestry proportions are similar / different to Laz 2016's Levant BA - the ancestral model populations are different).

Matt said...

Re: - "Corded Ware "more mobile than anything before or after" in Europe", looking at https://pbs.twimg.com/media/C8RorJSUwAEY3v9.jpg, looks like the vertical axis is social hierarchy - increases through all periods - while the horizontal is mobility - increases Early Neolithic to Late Neolithic, then flexes back to Middle Neolithic levels in the Bronze Age.

Couple of takes from this:

- Corded Ware here look like the continuation of Central European EN-MN trends of higher mobility, increased hierarchy. CWC is about as different from GAC (Globular Amphora), and in the same direction, as GAC is from LPC (Linear Pottery Culture). Even though Corded Ware's ancestry is predominantly not of the same stripe.

So take away is that Corded Ware Culture is not completely the "Big Bang" of a herding, pastoral lifestyle in Europe, imposed on a very static, settled Old Europe monolith, but part of a continued shift already ongoing through EN-MN. (Probably this is already well known to specialists). Despite the fact that CWC shows a reduction in local genetic continuity and complete replacement of the Y lineages.

(Wiki's presentation of Funnelbeaker Culture is as "dominated by animal husbandry of sheep, cattle, pigs and goats, but there was also hunting and fishing". Not really your people who lived off an almost purely grain and vegetable diet (a la the Roman Era https://phys.org/news/2017-03-tiller-hun-farmers-roman-empire.html), with stunted growth from low protein intake.)

- Bell Beaker which is more firmly in Bronze Age than Late Neolithic seems first to show a regress back to a more settled state in Central Europe. I have to wonder if this, compared to CWC, is a function of the production and use bronze tools and weapons favouring more settled societies? (Parallels of more metal using, settled Andronovo / Sintashta replacement of earlier, more mobile steppe groups?).

Ric Hern said...

I still get the feeling that something Proto-Indo-European was going on in or near Germany and Poland at roundabout 3300 BC. prior to Corded Ware Expansion.Why ? Because of the Salzmünde Tabiano coloured Horses and some other Archaeological oddities that points out Cultural changes during this time.The question that lingers in my mind is still: What happened to the Sredny Stog Culture ?

Arza said...

@ Matt

I have a feeling (maybe due to my bad English skills) that you have completely omitted the isochrones (?).

Maybe it wasn't a Big Bang, but CWC flew trough the Europe like a meteor.

CWC is about as different from GAC (Globular Amphora), and in the same direction, as GAC is from LPC (Linear Pottery Culture).

LPC → GAC - 4 (or even 5) periods = slow evolution, GAC practically stops in one place
GAC → CWC - same period in time = sudden increase of mobility

Matt said...

Yes, rate of change GAC>CWC and then CWC>BBC (sudden decrease in mobility), then BBC>EBA seems much more rapid than the LPC>FBC/GAC cultural changes would seem (though hard to tell all the dates of cultures in the graphic from the blurry shot). CWC enter relatively quickly, superceded relatively compared to preceding cultres.

Least hierarchial / least mobile FBC culture similar to most hierarchical / most mobile of adjacent group (LDG?). Not the case comparing CWC to GAC.

Rob said...

@Matt

"Despite the fact that CWC shows a reduction in local genetic continuity and complete replacement of the Y lineages"

I don't think thats the case. Rather, it's just that CWC *itself* seems to be very internally homogeneous from a Y lineage perspective

Matt said...

@ Rob, good point and probably a more correct way of talking about this (considering e.g. Unetice Culture and other later cultures).

Arza said...

Animated:
https://s18.postimg.org/6vuulaba1/mobility.gif
2.1 MB

ak2014b said...

Has anyone been able to successfully read all the mtDNA haplogroups found in the 90 ancient Egyptian mummy aDNA that are listed at Alexander M. Kim's twitter account at

https://pbs.twimg.com/media/C8Ril9lVoAEdkh1.jpg

The screen becomes less legible at the top for me, so from bottom to top I read

L0-L4, M5, N, ?, W, X, R?, R0, U, K, J, T?, ??, ??, H?, HV?

I'm inferring T, T1, T2 after J, but I can't be sure.


What I'm thinking of as T2, along with K and M5, disappear in the Ptolemaic period and reappear in the Roman period. Alternatively they just didn't turn up in the Ptolemaic samples.

The L2 or L3 disappears in the Roman period but was present in the periods before. Again, could be related to sampling.

Not sure if it has any meaning, but it seemed interesting since the other haplogroups didn't disappear from one period to the next.

Rob said...

@ Matt

Yes, CWC didn't just sweep through Europe. Careful maps illustrate "islands" of CWC, just like BB. Other cultures like TRB, Baden-TRB, GAC, Mesolithics did not simply vanish. They continued on until 2000 BC; when the Bronze Age begins in Northern Europe; and another round of changes began. This might explain why Unetice is niether mostly R1b nor R1a, but I2.

FYI that slide is from the seminal 2011 paper:
https://repozytorium.amu.edu.pl/bitstream/10593/14427/1/Eur24_12-Czebreszuk.pdf



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Matt said...

@Arza, that's what those faint lines mean then... Seems surprising that all the most mobile and most hierarchical sites in GAC (for ex) necessarily overlap temporally with CWC, etc. But I suppose if that is what is the case it is the case.

AWood said...

@Arza

Bell Beaker = Less Mobility ?
Are you sure about that one? IE or not, please take another look at the territory and expanse of Bell Beaker related industries.

jv said...

Thank you for the
"tweeted" information! Always interested in those CWC females and their migrations. CWC females=extreme mobility=spread of I.E. languages.

bellbeakerblogger said...

Isotopes would tell you 100% of Afrikaaners are native to South Africa, which is true depending on how the question is asked.
The high mobility within CWC should be expected because they are cattle trespassers and seasonal herders. That doesn't logically mean GAC is more native based on movement within an individual's​ lifetime.

epoch2013 said...

@bellbeakerblogger

"Isotopes would tell you 100% of Afrikaaners are native to South Africa"

One of the funnier things is, according to xyyman that is actually true.

John Smith said...

Does anybody have an idea of the y DNA of the mummies?

Labayu said...

@Aram

African admizture in Egypt and Levant is not only slave's legacy.

The Fatimid Black Africans soldiers were also slaves, raised from a young age to be soldiers.

Ryan said...

Random question but - does anyone have an idea on the statistics around DNA recombination? Like for example, an uncle/nephew should share 1700cM on average. What's the +/- on that? If someone shares 1600 are they definitely as related as uncle/nephew, or is an outlier for first cousin (850 cM) possible?

Karl_K said...

@Ryan

There can be a large variation in the statistics, even with siblings. But there are other ways to verify a relationship if necessary. Haplogroups help of course.

On several occasions, I have helped people determine the actual genetic relationship to an 'aunt' or 'half-sister' or a 'cousin'.

In many cases, you need to have additional data from another person who should be more related to one of the people than to the other person to be positive.

https://isogg.org/wiki/Autosomal_DNA_statistics

Karl_K said...

@Ryan

To be more clear. Yes, there is a bit of overlap between uncle/aunt and 1st cousin statistical relationships on the autosomal level.

Grey said...

Gihanga Rwanda said...
"I am honestly surprised, but how else can we explain the comparable levels of East African ancestry (~15%) found in both Copts and Egyptian Muslims?"

mummies = upper caste?

Ryan said...

@Karl - haplogroups won't help in this case. At 1,600 cM how likely do you think a first cousin relationship is?

Karl_K said...

@Ryan

It is extremely unlikely (<1% chance), but not impossible.

You need a closely related 3rd person that is related to them both but in a different way. A sibling, 1st-2nd cousin, parent, aunt, uncle, or similar.

Matt said...

BHG, nice. My various comments on the slides Kim has put for Damgaard's presentation (Alex if you're reading, much appreciated!):

- PCA: Not so clear how many samples are ancient / modern. Seems like too many ancients in Caucasus and East Asia for ex to feasibly all be ancient. But I may be hugely underestimating for many Armenian and Iron Age eastern steppe have now been amassed. Not sure why Corded Ware and no other Europe LNBA seems to be included but shouldn't matter for the construction. More seriously, I can't spot the Neolithic Iranians on there, unless they're under the Near East bucket, which could be more important.

I'd assume the samples outside of their limns of the black lines are their new BHG sample - https://pbs.twimg.com/media/C8XKypJVwAAUgF0.jpg.
Construction looks kind of minimally informative for intra-East Eurasian variation, given balance of samples (mainly West Eurasian and main axes are West->East and West Eurasia North->West Eurasia South), so would be cautious of inferring relatively low differentiation of present day BHG from present day East Eurasians.

- Comment: "The Baikal Hunter-Gathererers represent a relatively inbred group of individuals (unusually high average shared drift between individuals)". Sounds like further nice confirmation of my speculation that these individuals will have far higher outgroup f3 sharing with each other than modern groups do. In the same way that it has been noted that the WHG, SHG, El Miron, Boncuklu, CHG (essentially all ancient hg) are all extremely much more homogenous than any recent group. Also the same relatively low conditional nucleotide diversities and heterozygosities compared to present day people as found in WHG, Boncuklu, SHG.

I think you will need admixture to get to modern East Asian levels of within group f3 sharing, but it may turn out that little of this will necessarily be outside the ENA clade. (So present day East Asians as largely admixture between very differentiated ENA groups?).

- "Krause: Total replacement of hunter-gatherers in Cis-Baikal between about 15 & 7 or 8 kaBP?" - I wonder what the evidence for that is? Inconclusive D(Mbuti,Baikal15000BP)(Baikal7000BP,Pop) stats?

Matt said...

Also lack of WHG and SHG on the PCA from presentation of Damgaard's paper.

Ariel said...

Davidski

Could the Egyptian PCA have projection bias?

Davidski said...

If they ran that PCA in the usual way, by basing it on modern samples and projecting the ancient samples, then the results of the ancient samples will be biased relative to those of the modern samples.

However, projection bias isn't as much of a problem in inter-continental PCA like this one, because the differentiation they're based on is greater.

Also, the results of the ancient Egyptians aren't biased relative to those of the other ancient samples, like the Neolithic farmers from the Levant, who basically overlap with them.

So I'd say projection bias in this case shouldn't be much of an issue.

Simon_W said...

If I'm not completely wrong, the proponents of the theory of a SSA ancient Egypt and "black pharaohs" have argued on morphological grounds for a SSA affinity. In fact, the same thing has happened to the Natufians. For example, Coon wrote about the Natufians:
"The skulls which Keith describes are of a peculiarly Mediterranean type, with a cephalic index ranging from 72 to 78, thus rivalling the subdolichocephalic head form of short statured Mediterraneans living today. The brain cases are of medium size, and the faces absolutely small. The lower jaws are also small and weakly developed, with little chin prominence and a prevalence of alveolar prognathism. The wide, low-vaulted nose, in combination with prognathism, gives a somewhat negroid cast to the face. The browridges are smooth, and the whole system of muscularity in the male but slightly developed. These late Natufians represent a basically Mediterranean type with minor negroid affinities."

Now we know that the Natufians didn't have SSA affinity, but rather Basal Eurasian. And what looks "Negroid" about them isn't really Negroid. And apparently exactly the same applies to the Ancient Egyptians.

Andres Folg said...

Simon_W, Natufians are a mixed population of at least two or more populations. They had African E1b paternal background ("Negroid") and a mostly Eurasian mtDNA maternal background (non-"Negroid"). This E1b group is splitted thousands of years before from their contemporaneous SSA populations.

Simon_W said...

Yes, for sure they had E1b, but the origin of E1b is controversial afaik, and anyway, you can't use this evidence for autosomal admixture, as some Balkan populations also have lots of E1b, but no exceptional SSA admixture. Whether Natufians had more than trace level SSA affinity or not has to be demonstrated with formal stats, and as far as I've followed these discussions they didn't have noteworthy SSA admixture, but feel free to correct me.

Simon_W said...

According to David's Basal-rich K7, a Natufian HG had 0.65% SSA - that's trace level I'd say, so you can argue it was there, and I'd say OK, but it's for sure not the amount that would influence the facial morphology.
https://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit#gid=289082796

Story Teller said...

@Simon_W

So how do you explain this?

Second, we observed that all three Natufian individuals that could be assigned to a specific haplogroup belonged to haplogroup E1b1. This is thought to have an East African origin, and a 4,500-year old individual from the Ethiopian highlands 13 belonged to it.

[...]

"Previously, the West Eurasian population known to be the best proxy for this ancestry was present-day Sardinians, who resemble Neolithic Europeans genetically.

However, our analysis shows that East African ancestry is significantly better modelled by Levantine early farmers than by Anatolian or early European farmers, implying that the spread of this ancestry to East Africa was not from the same group that spread Near Eastern ancestry into Europe (Extended 283 Data Fig. 4; Supplementary Information, section 8)" [p. 9].
--Lazaridis et al.,

Mina said...

@Simon_W E1b1 (E-P2)

"The proto-Afro-Asiatic group carrying the E-P2 mutation may have appeared at this point in time and subsequently gave rise to the different major population groups including current speakers of the Afro-Asiatic languages and pastoralist populations.

[…]

Y-chromosome haplogroup tree

All the analyses in this study were done at the same resolution using the following 17 bi-allelic markers: E-M96, E-M33, E-P2, E-M2, E-M58, E-M191, E-M154, E-M329, E-M215, E-M35, E-M78, E-M81, E-M123, E-M34, E-V6, E-V16/E-M281 and E-M75.

[…]

The network cluster associated with the Eritrean Nilo-Saharan Kunama (Figure 1) may represent an expansion event following the out-of-Africa migration,31, 46 possibly close to the origin of the ancestral Y-chromosome clades.47, 48, 49 The expansion, carrying the diversified E-P2 mutation, may be responsible for the migration of male populations to different parts of the continent and henceforth the rise and spread of the bearers of the macrohaplogroup.50 These type of population movements, or demic expansions, driven by climatic change and/or spread of pastoralism and to some extent agriculture,51, 52, 53, 54 are not uncommon in human history. This scenario is more substantiated by the refining of the E-P2 (Trombetta et al35) and its two basal clades E-M2 and E-M329, which are believed to be prevalent exclusively in Western Africa and Eastern Africa, respectively.

[…]

The network result put North African populations like the Saharawi, Morocco Berbers and Arabs in a separate cluster. Given the proposed origin of Maghreb ancestors56, 57, 58, 59 in North Africa, our network dating suggested a divergence of North Western African populations from Eastern African as early as 32 000 YBP, which is close to the estimated dates to the origin of E-P2 macrohaplogroup."

—Eyoab I Gebremeskel1,2 and Muntaser E Ibrahim

Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism
EJHGOpen

European Journal of Human Genetics (2014) 22, 1387–1392; doi:10.1038/ejhg.2014.41; published online 26 March 2014

Mina said...

@Simon_W


http://i63.tinypic.com/10cmfl2.jpg

Fig. S7. f3(X, GD13a; Dinka) shows that the closest modern populations to GD13a are Caucasus populations and, to some extent, South Asian populations such as Balochi and Makrani. Map of populations was generated with the library “ggplot2” with R software


Dataset preparation for population genetic analyses
Genotypes were called in GD13a at sites which overlapped those in the Human Origins dataset (Lazaridis et al.17, filtered as described in Jones et al.24) using GATK Pileup44

The site has been directly dated to 9650)9950 calBP (11), showing intense occupation over two to three centuries. The economy of the population has been shown to be that of pastoralists, focusing on goats (11). Archaeobotanical evidence is limited (16) but the evidence present is for two)row barley, probably wild, and no evidence for wheat, rye or other domesticates. In other words the overall economy is divergent from the classic agricultural mode of cereal agriculture found in the Levant, Anatolia and Northern Mesopotamian basin.

[…]

We compared GD13a with a number of other ancient genomes and modern populations (6, 17–29), using principal component analysis (PCA) (30), ADMIXTURE (31) and outgroup f3 statistics (32) (Fig. 1). GD13a did not cluster with any other early Neolithic individual from Eurasia in any of the analyses. ADMIXTURE and outgroup f3 identified Caucasus Hunter)Gatherers of Western Georgia, just north of the Zagros mountains, as the group genetically most similar to GD13a (Fig. 1B&C), whilst PCA also revealed some affinity with modern Central South Asian populations such as Balochi, Makrani and Brahui (Fig. 1A and Fig. S4). Also genetically close to GD13a were ancient samples from Steppe populations (Yamanya & Afanasievo) that were part of one or more Bronze age migrations into Europe, as well as early Bronze age cultures in that continent (Corded Ware) (17, 23), in line with previous relationships observed for the Caucasus Hunter)Gatherers (26).

[...]

Figure Legends:

Fig. 1. GD13a appears to be related to Caucasus Hunter Gatherers and to modern South Asian populations.

A) PCA loaded on modern populations (represented by open symbols). Ancient individuals (solid symbols) are projected onto these axes.


B) Outgroup f3(X, GD13a; Dinka), where Caucasus Hunter Gatherers (Kotias and Satsurblia) share the most drift with GD13a. Ancient samples have filled circles whereas modern populations are represented by empty symbols.


C) ADMIXTURE using K=17, where GD13a appears very similar to Caucasus Hunter Gatherers, and to a lesser extent to modern south Asian populations.

S7. Outgroup f3 statistics show that GD13a shares the most genetic drift with Caucasus Hunter-gatherers


We used outgroup f3-statistics to estimate the amount of shared drift between GD13a and contemporary populations. This was performed on the dataset described in section S6 using the qp3Pop program in the ADMIXTOOLS package (13). We computed f3(X, GD13a; Dinka), where X represents a modern population and Dinka, an African population equally related to Eurasians, acts as an outgroup (Fig. S7). We also repeated this analysis where X represents ancient individuals/populations. Among the ancient populations, Caucasus hunter-gatherers (Kotias and Satsurblia) have the closest affinity to GD13a (Table S3), followed by other ancient individuals from Steppe populations from the Bronze age and modern populations from the Caucasus.

—M. Gallego-Llorente,

The genetics of an early Neolithic pastoralist from the Zagros, Iran

John Smith said...

You can not use a 4500 year old Individual to Infer where someone from 13,000kya came from!! You can not use Modern Frequencies without DIRECT ancient dna evidence to suggest where a Upper Paleolithic population lived or even a neolithic population at times as so many bronze age invasions happened! Did you forget C1a,C1b and K2a y-dna in Ancient Europe? Did you forget basal extinct branch of M mtdna in Europe around Belgium and Northern France? There was also M in southern Italy in the Upper to mid Paleolithic as a minority but I dont know if it was the same type. Would National geographic guess that C1a, C1b,K2a1 y-dna and M Mtdna was found in Upper Paleolithic Europe with their Coastal Migration facts?? The answer is NO! Before ancient dna it seemed clear E1b1b originated in Africa however the fact that they (Natufians) all had E1b1b so long ago and seemed to have little to weak Sub Saharan Affinity suggest it originated in the Levant or nearby froma source population with all N mtdna. Also IT is not a fact that humans come from Africa. It is possible but is is not a fact. It is a hypothesis until ancient dna evidence shows it happened or disproves it. Some Near Easterns have so little Neanderthal admixture and are less than 10% African that it means that some Eurasian Populations probably up until at least the Neolithic had no Neanderthal Admixture and the Neantheral Admixture happened in Populations that had links to the Far East e.g (Oase 1 with his NO type y-dna) https://www.quantamagazine.org/wp-content/uploads/2016/05/Where-the-hominids-roamed_1000.png. Did the Natufians have any Neanderthal Admixture? No one answers this question. Furthermore scientist exclude the possibility that a bottle neck probably from Toba could have killed various A,B and L lines in Eurasia but not Africa which would make SOME African populations espically those admixted with Eurasians more diverse where in fact Homo Sapiens Sapiens possibly originated in Eurasia. If you use one of those trees you would think that R1b is from Turkey and R1a is from Iran when according to ancient dna those are clearly incorrect assumptions.

Labayu said...

@Ryan

I would think a previously unknown relative with 1,600 cM in common is most likely a half sibling.

Rob said...

proto-Natufians probably expanded from northeast Africa but still have no SSA admixture
There's no issues there

Mina said...

@John Smith

The 13kya individuals carried the same gene pool as the 4.5 Kya individual.

Natufians

I0861: E1b1b1b2(x E1b1b1b2a, E1b1b1b2b)
I1069: E1b1(xE1b1a1, E1b1b1b1)
I1072: E1b1b1b2(xE1b1b1b2a, E1b1b1b2b)
I1685: CT
I1690: CT


Ofer Bar-Yosef cites the microburin technique and “microlithic forms such as arched backed bladelets and La Mouillah points" as well as the parthenocarpic figs found in Natufian territory originated in the Sudan.

--Bar-Yosef O., Pleistocene connections between Africa and South West Asia: an archaeological perspective. The African Archaeological Review; Chapter 5, pg 29-38; Kislev ME, Hartmann A, Bar-Yosef O, Early domesticated fig in the Jordan Valley. Nature 312:1372–1374.


Christopher Ehret noted that the intensive use of plants among the Natufians was first found in Africa, as a precursor to the development of farming in the Fertile Crescent.

--Ehret (2002) The Civilizations of Africa: A History to 1800. Charlottesville: University Press of Virginia



"Building on and refining stone tool typologies from North Africa,21,22 the foundation for EP research in the Levant was provided by O. Bar-Yosef23 in his seminal work identifying and defining EP cultures of the southern Levant based on these tools and other site features.

[...]

Early models of culture change associated with pre-agricultural societies of the Levant focused on the sudden, late origin of settled farming villages triggered by climate change. Accompanying this new economic and living situation was durable stone-built architecture; intensified plant and animal use; a flourishing of art and decoration; new mortuary traditions, including marked graves and cemeteries; elaborate ritual and symbolic behavior— a new way of life. This new life style arguably had a slow start, but really took off during the Epipaleolithic period (EP), spanning more than 10,000 years of Levantine prehistory from c. 23,000-11,500 cal BP. The last EP phase, immediately preceding the Neolithic, is by far the best-studied in terms of its cultural and economic contributions to questions on the origins of agriculture.

[...]

Figure 2 presents globally and locally recognized climatic events from 23,000 to 11,500 cal BP and the approximate dates for major EP phases.

[...]

In 2000, McBrearty and Brooks provided compelling evidence that the origin of modern human behavior was not an Upper Palaeolithic revolution, as it has often been interpreted, but that the components of modern human behavior developed over tens or even hundreds of thousands of years of prehistory within Africa.14 In the Near East, Gordon Childe coined the term ‘‘Neolithic revolution’’ to refer to the development of human control over the reproduction and evolution of plants and animals,111 which arguably was the single most significant social, cultural, and biological transition since the origin of our species."

--LISA A. MAHER, TOBIAS RICHTER, AND JAY T. STOCK

Evolutionary Anthropology 21:69–81 (2012)

The Pre-Natufian Epipaleolithic: Long-Term Behavioral Trends in the Levant


Mina said...

Rob

What do you mean by "proto-Natufians probably expanded from northeast Africa but still have no SSA admixture" There's no issues there"

What would the issue be?

Mina said...

@John Smith

"all had E1b1b so long ago and seemed to have little to weak Sub Saharan"


But they cluster with East Africans closely? lol smh


From where did you get this theory?

"in fact Homo Sapiens Sapiens possibly originated in Eurasia."


The Homo Sapiens Sapiens was found in East Africa. How do you explain the older tool industries in Africa? How do you explain the older genetic stems in Africa?


160,000-year-old fossilized skulls uncovered in Ethiopia are oldest anatomically modern humans

Ancient lake shore

The early humans at Herto lived along the shores of a shallow lake created when the Awash River temporarily dammed about 260,000 years ago. The lake contained abundant hippos, crocodiles and catfish, while buffalo roamed the land.

The sediments and volcanic rock in which the fossils were found were dated at between 160,000 and 154,000 years by a combination of two methods. The argon/argon method was used by colleagues in the Berkeley Geochronology Center, led by Paul R. Renne, a UC Berkeley adjunct professor of geology. WoldeGabriel of Los Alamos National Laboratory and Bill Hart of Miami University in Ohio used the chemistry of the volcanic layers to correlate the dated layers.


http://www.berkeley.edu/news/media/releases/2003/06/11_idaltu.shtml

John Smith said...

1.''The 13kya individuals carried the same gene pool as the 4.5 Kya individual''. Well I would assume that means a close relative of the 13kya individual is ancestral to the 4.5 individual at least partially as the 13kya individual is 8.5kya years older. Yes the evidence is E1b1b is from Africa according to modern Evidence but you just provided evidence that the E1b1b and maybe even E1b1 is from the Levant or Nearby according to ancient dna. If you find a 14.5kya indivudal from Ethiopia that theory goes out the window but a 4.5kya individual is not much better than a modern individual. You might be right maybe around at least a 50% chance but there is a chance you are wrong because we have no ancient dna proving that hypothesis.
If you look at genetiker the two CTs belonged to E1b1b as well papers always do a sloppy job on y-snp analysis.Some act like archaeological evidence is Important but please tell me any Archaeological evidence that would have suggested that K2a and C1a and C1b y-dna and M mtdna was found in upper Paleolithic Europe? Before the bronze age Archaeological evidence is almost worthless for finding ancient human migrations.
2. "proto-Natufians probably expanded from northeast Africa but still have no SSA admixture" There's no issues there" Yes that makes sense and the second part is proven but the first part is pure speculation. We would need ancient dna pre-Natufian from Northeast Africa to prove or disprove it. I think they were Indigenous and were in the Levant since at least 25kya but that is speculation as well.

John Smith said...

''160,000-year-old fossilized skulls uncovered in Ethiopia are oldest anatomically modern humans'' Thats pretty strong evidence but until we have ancient dna showing they were homo sapiens sapiens AND related to the group that is ancestral to moden humans its still a hypothesis. Correct me if I am wrong but if I understand correctly, Qafzeh and Skhul are 80,000-120,000 years old https://en.wikipedia.org/wiki/Skhul_and_Qafzeh_hominids (I know Wikipedia is not a good source but I have work and college and am limited in time). There could be older bones not found. We didnt know of Denisovans until ancient dna, maybe they were in Eurasia 200kya however like Denisovans they have no Skulls found.

The genetic stems are not older they are just more divergent from the main lines in Eurasia but not as divergent as Neanderthals or Denisovans. If scientist are so confident of these results why not study there dna? Are they afraid? As explained before this can easily be explained by a bottleneck in which most L mtdna and A and B lines in Eurasia died off due to Toba. I read Saudi Arabia due to politics is hard to dig in and if humans originated there we wouldn't know from bones because the government wont let us dig there, again I am limited in time so I don't have time to find the source and please correct me if I am wrong about this.

Maybe humans originated near the Persian Gulf see the Arabo-Persian Gulf Oasis Hypothesis.
''How do you explain the older genetic stems in Africa?'' In addition to the previous answer the main answer is people move. Modern populations are useless for telling where people lived 35+kya. As I explained many times C1a, C1b and K2a and M mtdna in Europe? Who guessed this? This is why I question the out of Africa Hypothesis. I did not before seeing these results.

I still think that modern humans possibly came from Africa but without ancient dna including ancient dna from Africa to prove or disprove it it is just a hypothesis and when more ancient remains are studied we may find a surprising story that no one would have guessed in a million years or maybe it will the mainstream is right or maybe something in between is all I am saying.

Basically all I am saying is I think that archaeology modern dna ect is useless for finding where humans came from and that ancient dna is the best and only way to tell.

John Smith said...

''"all had E1b1b so long ago and seemed to have little to weak Sub Saharan"
But they cluster with East Africans closely? lol smh ''

This seems to prove that East Africans come partially from Natufians. AFAIK this is almost a fact as E1b1b1b2 E-Z830 seems to come from Natufians and is common in East Africa if you read https://en.wikipedia.org/wiki/Haplogroup_E-Z827#E-Z830_.28E1b1b1b2.29. Datog (43%), Khwe (Kxoe) (31%), Burunge (28%), and Sandawe (24%) 14.7% among the Ethiopian Amhara, and 16.7% among the Ethiopian Wolayta. These populations have a y-dna line which was found in Natufians and probably is from Natufians beyond that we dont have enough ancient dna evidence to show where E1b1b or E1b1 is from ultimately.

Mina said...

@John Smith


How do you explain this?

Although Haplogroup M differentiated
soon after the out of Africa exit and it is
widely distributed in Asia (east Asia and
India) and Oceania, there is an
interesting exception for one of its more
than 40 sub-clades: M1 ... Indeed this
lineage is mainly limited to the African
continent with peaks in the Horn of
Africa."

--Paola Spinozzi, Alessandro Zironi

(2010). Origins as a Paradigm in the
Sciences and in the Humanities.
Vandenhoeck & Ruprecht. pp. 48-50

"These indicate that the root of L3 gives rise to a multifurcation from a single haplotype producing a number of distinct subclasses.... The simplest explanation for this geographical distribution [haplogroups M and N], however, is an expansion of the root type within East Africa, where several independent L3 branches thrive, including a sister group to L3, christened L4 (Kivisild et al. 2004; Chap. 7), followed by divergence into haplogroups M and N somewhere between the Horn of Africa and the Indian subcontinent. Since neither the L3 root type nor any other descendants survive outside Africa, the root type itself must have become extinct during a period of genetic drift in the founder population as it diversified into haplogroups M and N, if the diversification was outside Africa. If on the other hand the diversification was indeed within East Africa, then Haplogroups M and N must have either been carried out of Africa in their entirety or subsequently have become extinct within Africa, with the singular exception of the derived M1."

-- Hans-Jürgen Bandelt et. 2006. EDS. Human Mitochondrial DNA and the Evolution of Homo sapiens.



"Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/’hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100–150 kyr ago.In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80–100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.

[...]

Yet Khoisan populations have maintained the greatest nuclear-genetic diversity among all human populations3, 4, 5 and the most ancient Y-chromosome and mitochondrial DNA lineages6, 7, implying relatively larger effective population sizes for ancestral Khoisan populations."

http://www.nature.com/ncomms/2014/141204/ncomms6692/full/ncomms6692.html

Mina said...

@John Smith

"We would need ancient dna pre-Natufian from Northeast Africa to prove or disprove it. I think they were Indigenous and were in the Levant since at least 25kya but that is speculation as well."

Pre-Natufian tool industries came from Africa, as they moved into the Levant.

We also know that PN2 originated in East Africa, as was posted prior. See:

Eyoab I Gebremeskel1,2 and Muntaser E Ibrahim

Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism



"If you look at genetiker the two CTs belonged to E1b1b as well papers always do a sloppy job on y-snp analysis."


"This branching pattern, along with the geographical distribution of the major clades A, B, and CT, has been interpreted as supporting an African origin for anatomically modern humans,10 with Khoisan from south Africa and Ethiopians from east Africa sharing the deepest lineages of the phylogeny.15 and 16

[...]

http://ars.els-cdn.com/content/image/1-s2.0-S0002929711001649-gr1.jpg

The deepest branching separates A1b from a monophyletic clade whose members (A1a, A2, A3, B, C, and R) all share seven mutually reinforcing derived mutations (five transitions and two transversions, all at non-CpG sites).

[…]

http://ars.els-cdn.com/content/image/1-s2.0-S0002929711001649-gr2.jpg

How does the present MSY tree compare with the backbone of the recently published “reference” MSY phylogeny?13 The phylogenetic relationships we observed among chromosomes belonging to haplogroups B, C, and R are reminiscent of those reported in the tree by Karafet et al.13 These chromosomes belong to a clade (haplogroup BT) in which chromosomes C and R share a common ancestor (Figure 2)."

—Fulvio Cruciani et al

A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa (2011)

Mina said...

@John Smith

"This seems to prove that East Africans come partially from Natufians."

"These populations have a y-dna line which was found in Natufians and probably is from Natufians beyond that we dont have enough ancient dna evidence to show where E1b1b or E1b1 is from ultimately."

I am not sure how this fits, and how you came to that conclusion?

But we have tool industries form Africa as precursor for Natufians at the Levant and PN2 being from East Africa going back before there was any Natufian at the Levant. See: "Eyoab I Gebremeskel1,2 and Muntaser E Ibrahim

Y-chromosome E haplogroups: their distribution and implication to the origin of Afro-Asiatic languages and pastoralism"



"This finding is in agreement with morphological data that suggest that populations with sub-Saharan morphological elements were present in northeastern Africa, from the Paleolithic to at least the early Holocene, and diffused northward to the Levant and Anatolia beginning in the Mesolithic.

[...]

"From the Mesolithic to the early Neolithic period different lines of evidence support an out-of-Africa Mesolithic migration to the Levant by northeastern African groups that had biological affinities with sub-Saharan populations.  From a genetic point of view, several recent genetic studies have shown that sub-Lines: 369 to 3770.0pt PgVar Normal PagePgEnds: TEX [554],  Saharan genetic lineages (affiliated with the Y-chromosome PN2 clade; Underhill2 et al. 2001) have spread through Egypt into the Near East, the Mediterranean area, and, for some lineages, as far north as Turkey (E3b-M35 Y lineage; Cinniog¢lu et al. 2004; Luis et al. 2004), probably during several dispersal episodes since the Mesolithic (Cinniog¢lu et al. 2004; King et al. 2008; Lucotte and Mercier 2003;6 Luis et al. 2004; Quintana-Murci et al. 1999; Semino et al. 2004; Underhill et al.7 2001). This finding is in agreement with morphological data that suggest that populations with sub-Saharan morphological elements were present in northeastern Africa, from the Paleolithic to at least the early Holocene, and diffused northward10 to the Levant and Anatolia beginning in the Mesolithic. 

"Indeed, the rare and incomplete Paleolithic to early Neolithic skeletal specimens found in Egypt—such as the 33,000-year-old Nazlet Khater specimen (Pinhasi and Semal 2000), the Wadi Kubbaniya skeleton from the late Paleolithic site in the upper Nile valley (Wendorf et al. 1986), the Qarunian (Faiyum) early Neolithic crania (Henneberg et al. 1989; Midant-Reynes 2000), and the Nabta specimen from the Neolithic Nabta Playa site in the western desert of Egypt (Henneberg et al. 1980)—show, with regard to the great African biological diversity, similarities with some of the sub-Saharan middle Paleolithic and modern sub-Saharan specimens. This affinity pattern between ancient Egyptians and sub-Saharans has also been noticed by several other investigators (Angel 1972; Berry and Berry 1967, 1972; Keita 1995) and has been recently reinforced by the study of Brace et al. (2005), which clearly shows that the cranial morphology of prehistoric and recent northeast African populations is linked to sub-Saharan populations (Niger-Congo populations). These results support the hypothesis that some of the Paleolithic–early Holocene populations from northeast Africa were probably descendents of sub-Saharan ancestral populations."

--F X Ricaut · M Waelkens

Article: Cranial Discrete Traits in a Byzantine Population and Eastern Mediterranean Population Movements

Human Biology 11/2008; 80(5):535-64. DOI:10.3378/1534-6617-80.5.535 · 1.52 Impact Factor

Mina said...

@John Smith

"Basically all I am saying is I think that archaeology modern dna ect is useless for finding where humans came from and that ancient dna is the best and only way to tell."

In pop-genetics all compartments are needed, in order to get a clear picture.


http://www.pnas.org/content/109/44/17758/F2.medium.gif

"Colored dots indicate genetic diversity. Each new group outside of Africa represents a sampling of the genetic diversity present in its founder population. The ancestral population in Africa was sufficiently large to build up and retain substantial genetic diversity."

--Brenna M. Henna,
L. L. Cavalli-Sforzaa,1, and
Marcus W. Feldmanb,2
Edited by C. Owen Lovejoy, Kent State University, Kent, OH, and approved September 25, 2012 (received for review July 19, 2012)


Grey said...

Simo_W
"If I'm not completely wrong, the proponents of the theory of a SSA ancient Egypt and "black pharaohs" have argued on morphological grounds for a SSA affinity."

There's a history of Egyptians using Nubian/Kush for soldiers and (iirc) when Akehenaten tried to change the religion there was a successful invasion from the south but like Romans in Britain or Magyars in Hungary I guess these things don't always leave a genetic legacy.

John Smith said...

Basically you have a lot of old evidence supporting your views and you may be right I just want to encourage people to look at all the possibilities when they only have flimsy evidence so they dont think a hypothesis is a fact.
a. Concerning the Natufians the culture started 14,500 and they all had E1b1b the oldest discovered in the world, so maybe just Maybe E1b1b originated in the Levant or nearby more ancient dna evidence is needed to prove or disprove it even though your theory is strong (I.E the tool argument) it still could very well be wrong because it is not supported or rejected by ancient dna. I am not saying you are wrong I am just saying you might be wrong tools are not strong enough evidence ancient dna is.
b. Concerning your arguments of using modern haplogroups to infer the origins of ancient groups:
If people didnt move thousands of miles away from where modern populations live why was M mtdna (maybe even pre M1 in Italy? anyone have the Genbank for Ostuni 1) and K2a, C1a, C1b y-dna found in Europe if people would move 10,000 miles in one part of the world why wouldnt they in Another? What scientist do you know who forecasted these groups in Ancient Europe before ancient DNA using their diversity is origin nonsense? No matter how many times I ask you don't answer this question. Ancient dna all but proves U6 is from Europe.
c. Your hypothesis has the most support for RIGHT NOW but it is neither proven or disproven until ancient dna proves it or disproves it. Period.
d. Your arguments about archaeology and tools are very strong and they make me think you might be right but we still need ancient dna before it is even a theory. Your arguments about using modern populations to see where upper paleolithic populations lived are completely useless.
e. I agreed with the mainstream consensus but from the surprises I see in ancient dna especially from the upper paleolithic I really doubt they are true. If they knew so much why didn't they forecast these anomalies?
f. Explain the origin of D? E is very different from the rest of the Eurasians or the Eurasians but still that doesnt mean it originated in Africa or that it did not. I cant wait for more adna results.


John Smith said...

I am tired about arguing about things that no one knows about. It is like arguing about what Oase had before he was sequenced we would have guessed everything and debated everything except K2a. Does anyone have the genbank for Ostuni1 ? I want to know if she also had a dead type of M or the same type of M they had in Belgium or maybe a type of M which has modern relatives. If anyone has this info it would be greatly appreciated.

John Smith said...

I am not certain if this breaks the rules but I read them and I couldnt find that it does
if anyone finds the Nucloetide for Ostuni1 and it shows the mtdna she had I will pay you $5.

John Smith said...

Please explain A1a Cluster 1, M31+. found in Europe?

https://www.familytreedna.com/public/Haplogroup_A/default.aspx?section=yresults

I am not even certain that the most divergent lines are always found in Africa. This appears to be another blow to the OOW hypothesis. This is not the A3b that has ancestry in Ethiopia it is something much older and more divergent. It probably wasnt in paleolithic Europe because people moved so far and its not found in Ancient dna . I wonder where its from? Maybe Further East?

Onur Dinçer said...

@Mina

The 13kya individuals carried the same gene pool as the 4.5 Kya individual.

But they cluster with East Africans closely? lol smh


No, Natufians and Mota had very different gene pools. Natufians were genetically almost totally West Eurasian (Caucasoid) while Mota was almost totally Sub-Saharan African (Negroid) by genetics (see their autosomal results). Superficial similarities in Y-DNA haplogroups do not change this. Natufian-like affinity in some modern East African populations such as Ethiopians comes from their high levels of Natufian-like Caucasoid ancestry.

capra internetensis said...

@John Smith

According to YFull an A1a sample from Ireland has a TMRCA of about 12 000 years with samples from Gambia. It can be found in Moroccan Berbers as well as in northern West Africa. I'd guess it reached Europe from North Africa sometime in the Holocene, but who knows when exactly.

John Smith said...

Thats a relatively small TMRCA so that means its probably from North Africa. Perhaps it was the main line in North Africa before E1b1b (No ancient dna to prove this however). My hypothesis of paleolithic origins on it from the east is almost certainly incorrect however still no direct evidence exists of OOA which is a hypothesis.

capra internetensis said...

I actually agree with you that an Out-of-Southern-Eurasia hypothesis remains possible, since there is such a poor fossil record and in principle Toba could have wiped out all preceding diversity. However, Out-of-Africa seems more probable.

John Smith said...

True hopefully ancient dna will resolve it once and for all.

Ryukendo K said...
This comment has been removed by the author.
Earl P Snerd said...

@Mina

"Pre-Natufian tool industries came from Africa, as they moved into the Levant."


According to archaeologists the Natufian culture and every culture before it and after originated in the Levant. People have been citing Ofer Bar-Yosef on the African origins of Proto-Natufian far too long now. That has been outdated since 1993 at least. The origins of the Mushabian is in the Trans-Jordan Nizzanan industry.

John Smith said...

@ Ryukendo ''This seems to suggest that all East Eurasians are a mix of BHG with some generalized 'mixed west Eurasians'''
I always thought that was the case my hypothesis was that N and K2a are Caucasoid like and that C2 y-dna (formerly C3) and M mtdna is the East Eurasian component 'in this case Extreme East Eurasian' of course I am oversimplifying it but I always thought that was the case nice to see it published. Of course ancient dna Evidence suggest both components may have distinct relatives in upper paleolithic Europe.

Earl P Snerd said...

From the results of the Egyptian mummies their autosomal DNA was said to be largely of the Natufian component with low to moderate Iranian and Anatolian component. That sounds a lot like the results for the Levant Chalcolithic that seems to have been replaced during the Bronze Age. This would make the Egyptians distinct from later waves of Semitic people like the Hyksos and others.

Ryukendo K said...
This comment has been removed by the author.
rozenfag said...

@ Ryukendo K The samples are from Baikal-Hokkaido Archaeological project: http://bhap.artsrn.ualberta.ca/, the oldest samples are 8000 years old, approximately 6000 BC

John Smith said...

I don't think ''East and Southeast Asians could be a result of recent, almost uniform introgression of West Eurasian ancestry across the Asia-Pacific post-BHG'' do you? If so thats really Bizarre. I don't have an age for the hunters sorry. I just think the K2a and N component may have been pre-Caucasiod and the C2 and M is 'extreme East Eurasian'. This group maybe didn't have the latter component or as much of it which was in other Asians for many Millennia. I do NOT think Eastern Eurasians come from upper paleolithic Europe because the K2a is closer to the K2a in India the C is C1 and not C2 and the M is an extinct branch except maybe Ostuni which is a mystery. If any group comes from Upper Paleolithic Europe either the (Oase Ishim) or (Kostniki Goyet groups) its probably a component of the South Asians and maybe the Melanesians the second being a stretch definitely not from the (Oase Ishim cluster)but maybe from a older(Kostenki Goyet cluster) possibly without one without U2 (maybe at least two groups formed the Augnicaians). The latter has little direct evidence but it would make sense. They may also be ancestral to a component off Western Eurasians as well. Or maybe they are completely extinct. I wouldn't be surprised if this 'extreme East Eurasian' population will have all C2 y-dna and M mtdna. Does any one know what y-dna and mtdna they had? Of course I may be incorrect by relying to much on uni-paternal lines.

John Smith said...

I am aware the Ishim was not in Europe but he has a brother Oase which makes me think he may have been on the Eastern group of his tribe.

Karl_K said...

Yes. And in that case haplogroups and the X chromosome can often clarify which parent is shared. I thought Ryan said haplogroups were not helpful, maybe he meant unavailable.

Ryukendo K said...
This comment has been removed by the author.
Salden said...

Go spam your Negrocentricism elsewhere. Natufians have already been to shown to have ultimately nothing when it comes to Tropical African admixture and were a West Eurasian population. East Africans and Horners are seriously admixtured with West Eurasians. And this has happened well before the Arabian Conquests so you can't try to dump that on it.

Ryukendo K said...
This comment has been removed by the author.
Samuel Andrews said...

@Earl,
" moderate Iranian and Anatolian component. That sounds a lot like the results for the Levant Chalcolithic that seems to have been replaced during the Bronze Age"

The Egyptians cluster near Bronze age Levanties in that PCA. Chalcolithic and Bronze age Levanties will probably come out basically the same.

Samuel Andrews said...

I posted about ancient Siberian(inclu. Lake Baikal) mtDNA a few weeks ago.

http://mtdnaatlas.blogspot.com/2017/03/siberia-past-and-present.html

Lake Baikal has no special mtDNA link to Ulchi. Most Ulchi mtDNA belongs to clades not found in Lake Baikal's ancient samples. But maybe Ulchi mtDNA is dominated by founder effects.

jparada said...

@John Smith

do you realize Oase doesn't show any special affinity either to Ust Ishim or to later Europeans? this means K2a can't be taken as a "Proto-Caucasoid" marker, or actually anything else beyond a generalized non-Basal Eurasian. It's actually more likely that Y-haplogroup R ultimately descends from a haplogroup originally found among a population of "Eastern Eurasian" affinities, given that it is found first among ANE, which was shown to be East Eurasian admixed on this paper

https://academic.oup.com/mbe/article/34/4/889/2838774/A-Working-Model-of-the-Deep-Relationships-of

Matt said...

RK: Nobody is commenting on the 'extreme East Eurasian' position of the Baikal Hunter Gatherers? This seems to suggest that all East Eurasians are a mix of BHG with some generalized 'mixed west Eurasians'.

Well, the comment here is "at the extreme of East Eurasian variation" so I would not take that to mean beyond the limits of populations today necessarily.

That said, even if we are talking about a population that is in a sense "More East Eurasian than East Eurasians", it doesn't mean that later East Eurasians are mixed with West Eurasians. There could be some distinct kind of ENA branch influx.

jparada said...

That said, even if we are talking about a population that is in a sense "More East Eurasian than East Eurasians", it doesn't mean that later East Eurasians are mixed with West Eurasians. There could be some distinct kind of ENA branch influx.

Actually, i wonder if modern East Asians don't carry trace levels of BA Steppe type ancestry. What made me wonder this is the odd East Asian affinity shown by the GoyetQ116-1 genome on the Ice Age Europe paper. The same paper shows this same individual is partially ancestral to Mesolithic Europeans (and so, by extension, to BA Steppe groups). So unless the particular Palaeoeuropean population this individual belonged to carried some unusual affinity to ancestral East Asians, the only explanation i can find for this result is that Steppe groups introduced this kind of ancestry in modern East Asians.

John Smith said...

I wouldn't expect Oase to have affinity to Europe he had K2a pre NO a different branch of course and not K2b which includes R. I

John Smith said...

Would expect Goyet to have affinity to the east as they are a population with C1a y DNA and M mtdna. My theory is M and C is East Eurasian and N and K are Eurasian Eurasian eg relatedness to IJ

Onur Dinçer said...

http://www.nature.com/nature/journal/v534/n7606/fig_tab/nature17993_ST1.html

The tested pre-LGM and post-Oase Upper Paleolithic Homo sapiens genomes from Europe, which have all turned out to be autosomally fully within the West Eurasian genetic variation with no discernable autosomal influence from outside the Caucasoid (West Eurasian) range, harbored Y-DNA C1 and mtDNA M haplogroups in non-negligible frequencies according to the results of the Fu et al. 2016 paper (see the table in the above link), so we can conclude that some sub-haplogroups of Y-DNA C1 and mtDNA M were parts of the Caucasoid or Proto-Caucasoid gene pool in those times (Y-DNA C1 continued to be so even after the LGM).

Earl P Snerd said...

@Samuel Andrews

I was referring to that new abstract that said the Levantine Chalcolithic was genetically distinct from the Bronze Age Levantines. In that abstract they said that the Levantine Chalcolithic had 58% Natufian component, 24% Anatolian component, and 14% Iranian component and that they were a dead end. From what was said about the ancient Egyptians, that they had a significant Natufian component and lower Anatolian and Iranian component, it sounds like the ancient Egyptians are similar to a pre-Bronze Age population from the Levant and are distinguished from Semitic people that came to Egypt later.

astenb said...

@Salden Few questions..
1 - Would you hypothesize that the E lineages found in Natufian are ultimately of North African origin?
2 - Do you expect These Egyptian samples, or older published samples to also carry E lineages?

Knight said...

@Salden
These samples are taken from Middle Egypt not Northern Egypt. It is taken from Fayum in Middle Egypt.