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Gravetto-Danubian
11-16-2015, 11:16 AM
Late Palaeolithic DNA from Georgian specimens sampled by the Dublin team has found the "Teal" that we have been looking for. ?

http://m.phys.org/news/2015-11-fourth-strand-european-ancestry-hunter-gatherers.html

Davidksi states on his blog that the full paper might be coming out later today !

-> full paper http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html




However, the sequencing of ancient DNA recovered from two separate burials in Western Georgia - one over 13,000 years old, the other almost 10,000 years old - has enabled scientists to reveal that the Yamnaya owed half their ancestry to previously unknown and genetically distinct hunter-gatherer sources: the fourth strand.

By reading the DNA, the researchers were able to show that the lineage of this fourth Caucasus hunter-gatherer strand diverged from the western hunter-gatherers just after the expansion of anatomically modern humans into Europe from Africa.

The Caucasus hunter-gatherer genome showed a continued mixture with the ancestors of the early farmers in the Levant area, which Manica says makes sense given the relative proximity. This ends, however, around 25,000 years ago - just before the time of the last glacial maximum, or peak Ice Age.

At this point, Caucasus hunter-gatherer populations shrink as the genes homogenise, a sign of breeding between those with increasingly similar DNA. This doesn't change for thousands of years as these populations remain in apparent isolation in the shelter of the mountains - possibly cut off from other major ancestral populations for as long as 15,000 years - until migrations began again as the Glacial Maximum recedes, and the Yamnaya culture ultimately emerges.

"We knew that the Yamnaya had this big genetic component that we couldn't place, and we can now see it was this ancient lineage hiding in the Caucasus during the last Ice Age," said Manica.

While the Caucasus hunter-gatherer ancestry would eventually be carried west by the Yamnaya, the researchers found it also had a significant influence further east. A similar population must have migrated into South Asia at some point, says Eppie Jones, a PhD student from Trinity College who is the first author of the paper.

"India is a complete mix of Asian and European genetic components. The Caucasus hunter-gatherer ancestry is the best match we've found for the European genetic component found right across modern Indian populations," Jones said. Researchers say this strand of ancestry may have flowed into the region with the bringers of Indo-Aryan languages.

The widespread nature of the Caucasus hunter-gatherer ancestry following its long isolation makes sense geographically, says Professor Ron Pinhasi, a lead senior author from University College Dublin. "The Caucasus region sits almost at a crossroads of the Eurasian landmass, with arguably the most sensible migration routes both west and east in the vicinity



ADD: the full paper is now out http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html

Gravetto-Danubian
11-16-2015, 11:18 AM
It is also interesting to note that they argue that it is this distinct branch which contributed to modern Indo Aryans. One wonders how Far East this Group had extended before the Bronze Age

Generalissimo
11-16-2015, 11:23 AM
It is also interesting to note that they argue that it is this distinct branch which contributed to modern Indo Aryans. One wonders how Far East this Group had extended before the Bronze Age

It might have first expanded with proto-Dravidians from Iran, and then again from the steppe with the Indo-Aryans.

Dubhthach
11-16-2015, 11:27 AM
Good to see folks at UCD (University College Dublin) and TCD (Trinity College Dublin -- oldest university in Ireland) involved in this. Bradley has mentioned in his talk in Dublin (or so I hear) that he had multiple samples from Mesolithic/BA/IA from Ireland so hopefully we'll see paper from them soon as well.

Gravetto-Danubian
11-16-2015, 11:27 AM
It might have first expanded with proto-Dravidians from Iran, and then again from the steppe with the Indo-Aryans.

I think we will find out very soon ;)

parastais
11-16-2015, 11:47 AM
So, teal farmers were actually local Caucasian isolated hunters... Is there any other way to interpret this?

Gravetto-Danubian
11-16-2015, 11:53 AM
So, teal farmers were actually local Caucasian isolated hunters... Is there any other way to interpret this?

Well they were hunters in the Palaeolithic, yes. By the Copper Age, the south Caucasus had a very diverse economy consisting of both Pastoral and farming elements. People often erroneously think anything south of the caucuses is automatically and exclusively "farming". This is incorrect

This population then moved to the north caucuses circa 4200 BC – the start of the pre-Majkop phase, and then gradually mixed with the EHG groups between 4000-3000 BC.

Heber
11-16-2015, 12:10 PM
Good to see folks at UCD (University College Dublin) and TCD (Trinity College Dublin -- oldest university in Ireland) involved in this. Bradley has mentioned in his talk in Dublin (or so I hear) that he had multiple samples from Mesolithic/BA/IA from Ireland so hopefully we'll see paper from them soon as well.

This is a joint project between TCD (Bradley) and UCD (Pinhasy).

They have nearly 1,000 ancient DNA samples many from the Hungarian Plain and about 20 from Ireland.

https://www.pinterest.com/gerardcorcoran/ancient-dna/

"Professor Bradley, leader of the Trinity team, said: "This is a major new piece in the human ancestry jigsaw, the influence of which is now present within almost all populations from the European continent and many beyond."

"The sequencing of genomes from this key region will have a major impact on the fields of palaeogeneomics and human evolution in Eurasia, as it bridges a major geographic gap in our knowledge," added Professor Ron Pinhasi, University College Dublin."

http://www.eurekalert.org/pub_releases/2015-11/tcd-sfi111315.php

Gravetto-Danubian
11-16-2015, 12:14 PM
The paper is out now and free to view

http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html

Happy reading !

Gravetto-Danubian
11-16-2015, 12:15 PM
This is a joint project between TCD (Bradley) and UCD (Pinhasy).

They have nearly 1,000 ancient DNA samples many from the Hungarian Plain and about 20 from Ireland.

https://www.pinterest.com/gerardcorcoran/ancient-dna/

"Professor Bradley, leader of the Trinity team, said: "This is a major new piece in the human ancestry jigsaw, the influence of which is now present within almost all populations from the European continent and many beyond."

"The sequencing of genomes from this key region will have a major impact on the fields of palaeogeneomics and human evolution in Eurasia, as it bridges a major geographic gap in our knowledge," added Professor Ron Pinhasi, University College Dublin."

http://www.eurekalert.org/pub_releases/2015-11/tcd-sfi111315.php

And they're all really nice people
Must be an Irish thing

Arame
11-16-2015, 12:27 PM
Teal is a reality !

Y DNAs are J and J2

MfA
11-16-2015, 12:32 PM
mtDNA
Kotias (9,529–9,895 cal. BP), Georgia - H13c
Satsurblia (13,132–13,380 cal. BP), Georgia - K3
Bichon (13,560–13,770 cal. BP), Switzerland - U5b1h

http://i.imgur.com/LxkyUkV.png

Gravetto-Danubian
11-16-2015, 12:37 PM
Teal is a reality !

Y DNAs are J and J2

And an I2a from Bichon

Jean M
11-16-2015, 12:44 PM
The paper is out: http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html

Jones et al., Upper Palaeolithic genomes reveal deep roots of modern Eurasians, Nature Communications, 6, Article number: 8912.

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

[Added] - Sorry! I was slow off the draw there. Trying to do several things at once. :)

rms2
11-16-2015, 12:56 PM
And an I2a from Bichon

Interesting that they describe him as a Cro-Magnon (". . . a young male of Cro-magnon type").

Heber
11-16-2015, 12:56 PM
CHG origins of migrating Early Bronze Age herders
We investigated the temporal stratigraphy of CHG influence by comparing these data to previously published ancient genomes. We find that CHG, or a population close to them, contributed to the genetic makeup of individuals from the Yamnaya culture, which have been implicated as vectors for the profound influx of Pontic steppe ancestry that spread westwards into Europe and east into central Asia with metallurgy, horseriding and probably Indo-European languages in the third millenium BC5, 7. CHG ancestry in these groups is supported by ADMIXTURE analysis (Fig. 1b) and admixture f3-statistics14, 25 (Fig. 5), which best describe the Yamnaya as a mix of CHG and Eastern European hunter-gatherers. The Yamnaya were semi-nomadic pastoralists, mainly dependent on stock-keeping but with some evidence for agriculture, including incorporation of a plow into one burial26. As such it is interesting that they lack an ancestral coefficient of the EF genome (Fig. 1b), which permeates through western European Neolithic and subsequent agricultural populations. During the Early Bronze Age, the Caucasus was in communication with the steppe, particularly via the Maikop culture27, which emerged in the first-half of the fourth millennium BC. The Maikop culture predated and, possibly with earlier southern influences, contributed to the formation of the adjacent Yamnaya culture that emerged further to the north and may be a candidate for the transmission of CHG ancestry. In the ADMIXTURE analysis of later ancient genomes (Fig. 1b) the Caucasus component gives a marker for the extension of Yamnaya admixture, with substantial contribution to both western and eastern Bronze Age samples. However, this is not completely coincident with metallurgy; Copper Age genomes from Northern Italy and Hungary show no contribution; neither does the earlier of two Hungarian Bronze Age individuals.

http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html

This was proposed by Cunliffe in his latest book, "Steppes, Desert and Ocean".

6637

https://www.pinterest.com/gerardcorcoran/steppes-desert-and-ocean/

https://www.pinterest.com/gerardcorcoran/ancient-dna/

MfA
11-16-2015, 12:57 PM
Modern impact of CHG ancestry.
In modern populations, the impact of CHG also stretches beyond Europe to the east. Central and South Asian populations received genetic influx from CHG (or a population close to them), as shown by a prominent CHG component in ADMIXTURE (Supplementary Fig. 5; Supplementary Note 9) and Admixture f3-statistics, which show many samples as a mix of CHG and another South Asian population (Fig. 4b; Supplementary Table 9). It has been proposed that modern Indians are a mixture of two ancestral components, an Ancestral North Indian component related to modern West Eurasians and an Ancestral South Indian component related more distantly to the Onge; here Kotias proves the majority best surrogate for the former(Supplementary Table 10). It is estimated that this admixture in the ancestors of Indian populations occurred relatively recently, 1,900–4,200 years BP, and is possibly linked with migrations introducing Indo-European languages and Vedic religion to the region.

Lank
11-16-2015, 01:14 PM
What do you guys think about the lack of an ANE (MA1) affinity in the paper?

Also, did CHG lack Basal Eurasian? If they lacked it, despite their relatively low divergence from EF, this would imply that Basal Eurasian in the Near East is from a relatively recent influx (from North Africa?).

I also wonder if the J Y-DNA implies that CHG or related populations are responsible for the spread of J.

Coldmountains
11-16-2015, 01:18 PM
Can anyone look at the supplementary figure 5? The resolution is too low when i zoom

MfA
11-16-2015, 01:42 PM
Both EHG dudes score some CHG on ADMIXTURE plot, Karelian HG's ancestors could be the ones are responsible for.

persian
11-16-2015, 01:46 PM
Are the authors not being too quick in their assessment of the isolation of these CHG without DNA from the southern Caspian? What makes them believe that these populations were isolated only in the Caucasus, without DNA from the East they shouldn't make such conclusions, unless ofcourse they know something we don't.

jdean
11-16-2015, 01:49 PM
Teal is a reality !

Y DNAs are J and J2

Brilliant : )

ADW_1981
11-16-2015, 01:54 PM
Good earlier prediction by David on his blog. This explains why the proto-EEF to this point have been predominantly H2, G, and WHG YDNA. Only a single J2 appeared in NW Anatolian farmers. These G + J2 guys were distinct groups for a very long time before eventually merging in the Middle East. We see that modern Caucasian Mountain populations are predominantly J and G, and now it make sense that they've been lingering in the region for an extremely long time.

More and more R1b, and R1a seem like a more recent layer of elite dominance on other populations. Pretty hard to deny now.

Tomenable
11-16-2015, 02:11 PM
Here is a previous paper (from 2014) with the same samples from the same sites in Georgia:

"Satsurblia: New Insights of Human Response and Survival across the Last Glacial Maximum in the Southern Caucasus":

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111271

Tomenable
11-16-2015, 02:17 PM
It seems, that EHGs and CHGs shared haplogroup J:

EHG, 3 samples of Y-DNA - R1b, R1a, J
CHG, 2 samples of Y-DNA - J, J2

Tomenable
11-16-2015, 02:26 PM
Both EHG dudes score some CHG on ADMIXTURE plot, Karelian HG's ancestors could be the ones are responsible for.

So EHGs score some CHG, but do not score any Teal ??? How is that possible considering that apparently Teal = CHG ???

Tomenable
11-16-2015, 02:28 PM
Bicicleur has had a theory, that Y-DNA haplogroup I came to Europe in Paleolithic times after crossing the Caucasus. He claimed, that it was haplogroup IJ which reached Caucasus region, where it subsequently split into I and J - and after that I moved on, entering Europe (and becoming the main lineage of WHGs), while J initially stayed in Caucasus region (becoming CHGs). His theory is now confirmed, it seems.

Tomenable
11-16-2015, 03:31 PM
EHG, CHG and AEF (Anatolian Early Farmers) autosomal groups and their Y-DNA:

Unfortunately vast areas still remain completely unsampled for ancient DNA.

http://s17.postimg.org/y4i4vf4bj/EHG_CHG_AEF.png

MfA
11-16-2015, 03:37 PM
So EHGs score some CHG, but do not score any Teal ??? How is that possible considering that apparently Teal = CHG ???

EHG did actually score some Teal, but back then it was thought a case of EHG-related admixture in Teal.
http://abload.de/img/ehg5ezl5.png
^it is taken from Haak et al. ADMIXTURE table.

MfA
11-16-2015, 03:40 PM
Are the authors not being too quick in their assessment of the isolation of these CHG without DNA from the southern Caspian? What makes them believe that these populations were isolated only in the Caucasus, without DNA from the East they shouldn't make such conclusions, unless ofcourse they know something we don't.

Epipaleolithic-Mesolithic Bradost, Zarzian and Caucasian cultures are archaeologically related.

Piquerobi
11-16-2015, 03:42 PM
The Gedrosia component of Dodecad? Or something which is related to Gedrosia?

Dodecad Oracle k12b results of Yamnaya:


Kit M020637 (Yamnaya_Sok_River I0443), the main components were the North European and the Gedrosia ones. Gedrosia is missing in ancient Western Europeans, Mesolithic and Neolithic, so an IE origin is a possible explanation. So the Gedrosia component would be useful in tracking IE expansions in Western Europe.

Dodecad K12b Oracle results:
Admix Results (sorted):

# Population Percent
1 North_European 60.8
2 Gedrosia 27.41
3 Atlantic_Med 5.95
4 Caucasus 2.92
5 Siberian 2.73
6 Sub_Saharan 0.18

RCO
11-16-2015, 04:08 PM
Are the authors not being too quick in their assessment of the isolation of these CHG without DNA from the southern Caspian? What makes them believe that these populations were isolated only in the Caucasus, without DNA from the East they shouldn't make such conclusions, unless ofcourse they know something we don't.

Yes, we need the Caspian and Northern Iranian samples to observe an entire Northern Near Eastern Hunther-Gatherer complex and of course ancient basal J1 also was there as we have been saying for years.

Dubhthach
11-16-2015, 04:18 PM
Are these the oldest Haplogroup J specimens so far found? They should at least provide a baseline for further research into J that's for sure.

Agamemnon
11-16-2015, 04:29 PM
Are these the oldest Haplogroup J specimens so far found? They should at least provide a baseline for further research into J that's for sure.

Yup, these are the oldest J specimens so far. But if we are to pinpoint J's origins, we'll need a lot more ancient data from the Transcaucasus and Middle East, this is just the beginning.

Jean M
11-16-2015, 04:30 PM
Are these the oldest Haplogroup J specimens so far found? They should at least provide a baseline for further research into J that's for sure.

They are indeed. The results are now up in my online tables:
http://www.ancestraljourneys.org/palaeolithicdna.shtml
http://www.ancestraljourneys.org/mesolithicdna.shtml

Dubhthach
11-16-2015, 04:47 PM
Yup, these are the oldest J specimens so far. But if we are to pinpoint J's origins, we'll need a lot more ancient data from the Transcaucasus and Middle East, this is just the beginning.

Indeed but as the "Seanfhocail" ("OldWord" eg. proverb) states:
tús maith leath na hOibre (Good start is half the work)

The Swiss find is also great as it's the oldest Haplogroup I so far sequenced. Papers like this hopefully are tip of Tsunami of aDNA data about to break on us.

Padre Organtino
11-16-2015, 05:04 PM
If you scroll back in time the first admixture runs you'll see how Georgians are modeled as West Asian plus Mediterranean while North Caucasians as West Asian plus Northern Euro.

Well, after getting hands on ancient genomes we come full circle. Judging from the PCA plot in the study Georgians are pretty much ENF plus these Teal guys.

Shaikorth
11-16-2015, 05:16 PM
The strongest f3 admixture signals North Caucasians get in this study don't involve Caucasus Hunter-Gatherers but LBK and MA-1 (Lezgins) or Karitiana/Nganasan (the rest).

Caucasus HG + LBK is the strongest stat only for Abkhazians, Georgians, Armenians and, maybe surprisingly, Cypriots.

Kale
11-16-2015, 05:16 PM
I wish they did some more stats using CHG against Ust-Ishim and others...I've been suspecting there is a third branch of crown eurasians that contributed to Caucasus and Central Asian ancestry, CHG looks like it (+basal Eurasian), but they only did stats to show CHG as more or less equidistant to various West Eurasians.

...Also is there a READABLE version of the admixture graph from this paper anywhere?

Agamemnon
11-16-2015, 05:19 PM
The strongest f3 admixture signals North Caucasians get in this study don't involve Caucasus Hunter-Gatherers but LBK and MA-1 (Lezgins) or Karitiana/Nganasan (the rest).

Caucasus HG + LBK is the strongest stat only for Abkhazians, Georgians, Armenians and, maybe surprisingly, Cypriots.

Truth be told, I don't find the Cypriots' presence surprising at all.

ADW_1981
11-16-2015, 06:00 PM
I wouldn't read too much into the J guy found amongst the EHG steppe cultures, or north Eurasian groups. If J2 was in the Caucasus mountains 13,000 ybp, I'm certain a gradual contact zone was setup between these regions. Since the Caucasus region holds a very high J2 variation and rare branches, the one amongst the EHG folks is likely related to the Caucasus branches. The more common J2a branches found in southern Europe and the middle east likely have a different cultural origin. A similar example would be how G-P303 found amongst the Anatolian farmer might be closer in relation to the successful lineages of P303 in Europe, and the Oetzi line is practically defunct.

EDITED: J2 -> J as correction ;)

Leeroy Jenkins
11-16-2015, 06:06 PM
I wouldn't read too much into the J2 guy found amongst the EHG steppe cultures, or north Eurasian groups. If J2 was in the Caucasus mountains 13,000 ybp, I'm certain a gradual contact zone was setup between these regions. Since the Caucasus region holds a very high J2 variation and rare branches, the one amongst the EHG folks is likely related to the Caucasus branches. The more common J2a branches found in southern Europe and the middle east likely have a different cultural origin. A similar example would be how G-P303 found amongst the Anatolian farmer might be closer in relation to the successful lineages of P303 in Europe, and the Oetzi line is practically defunct.

Just for clarification, it wasn't J2 found in the Karelian EHG, but J. I too doubt that particular J lineage was successful and agree with the rest of your post.

R.Rocca
11-16-2015, 06:36 PM
Very interesting quote from the paper and yet another circumstantial blow to the Anatolian Farming PIE expansion theory IMO (if you read into it enough)...


Surprisingly, we find that CHG influence is
stronger in northern than Southern Europe (Fig. 4a and
Supplementary Fig. 3A) despite the closer relationship between
CHG and EF compared with WHG, suggesting an increase of
CHG ancestry in Western Europeans subsequent to the early
Neolithic period. We investigated this further using D-statistics of
the form D(Yoruba, Kotias; EF, modern Western European
population), which confirmed a significant introgression from
CHG into modern northern European genomes after the early
Neolithic period

parasar
11-16-2015, 07:07 PM
Four South Asian populations are showing non negative f3
Kharia
Kusunda
Ongee
Kalash

Kalash South Asia Kotias Cabecar 0.016 0.001 11.166
Kharia South Asia Lahu Mala 0.001 0.000 2.675
Kusunda South Asia LBK_EN (I0054) Naxi 0.010 0.001 9.149
Onge South Asia Cambodian Papuan 0.130 0.002 61.297

Kharia are Austro Asiatic speaking.
The Kalash are IE isolates.
The Ongee are of course off the chart isolates.
The Kusunda are another Indo-Pacific population like the Ongee.
http://www.pnas.org/content/101/15/5692.full
"The Indo-Pacific family historically occupied a vast area from the Andaman Islands in the Indian Ocean to the Solomon Islands in the Pacific. Today most Indo-Pacific languages are found on New Guinea, where there are >700 surviving languages. Most of the western languages have disappeared as a consequence of the Austronesian expansion, but several ancient branches have survived on the Andaman Islands, the North Moluccas (North Halmahera and its smaller neighbors), and the lesser Sundas (Timor, Alor, and Pantar). East of New Guinea, Indo-Pacific languages survive on New Britain, New Ireland, the Solomon Islands, Rossel Island, and the Santa Cruz Islands. They also were spoken in Tasmania until 1876. The distribution of Kusunda and the Indo-Pacific family is shown in Fig. 1. Although it is not possible with present evidence to demonstrate conclusively the direction of the migration that separated Kusunda from the other Indo-Pacific languages, it would seem at least plausible that Kusunda is a remnant of the original migration to New Guinea and Australia rather than a backtracking to Nepal from the region in which other Indo-Pacific languages are spoken currently."
http://www.pnas.org/content/101/15/5692/F1.large.jpg
Fig. 1.
Location of Indo-Pacific languages. K, Kusunda; A, Andaman Islands; H, Halmahera; T, Timor-Alor-Pantar; NG, New Guinea; NB, New Britain; NI, New Ireland; SI, Solomon Islands; SC, Santa Cruz Islands; R, Rossel Island; TS, Tasmania.



No Dravidians have non-negative f3. The Dravidians are CHG(Kotias)+Kharia. This the basic structure of South Asia. So essentially we would have to pick one of these - Dravidian or Austro-Asiatic - as the native population of South Asia. The former are in large part F-H,L,J. The latter are about 50% O-M95.

Indo-Europeans in South Asia are similar to Dravidians but with a distinction once D stats are brought to bear; IE lean towards the Afanasievo_BA rather than Kotias. So Indo-Europeans would seem to have an amount of steppe input which came in with Y-R.

The Kusunda, I assume, are like the Ongee - a very early substrate that disappeared, or are migrants from SE Asia. Perhaps they were initially Y-D that we still see in the Andamans.

Between CHG(Kotias) and Kharia, one way to resolve which group is older in South Asia, would be figure out whether H-M3035 or O-M95 is older in South Asia.

"H-M3035 that now incorporates South Asian lineages H1-M69 (predominantly found in Indian peninsula), H2-B108 (detected in one of our Burmese samples) and H3-Z5857 (India)"
"In haplogroup O, common in Southeast and East Asia, our revised nomenclature recognizes seven basic subclades, O1-O7, that descend from the MRCA of O at ca 35 kya. O2a, which is common among Austro-Asiatic populations, is characterized by low diversity (MRCA 10.8, 95% CI 7.4-14.3 ky) and is composed of two major branches, O2a1 and O2a2 that are both 5-7 ky old (Figure S3, Table S7). Albeit significantly younger than earlier Y-STR based age estimates of
17-28 kya (Chaubey et al. 2011), the age estimates of O2a1 and O2a2 are broadly consistent with the dates associated with the spread of rice in SE Asia"
http://www.nature.com/ncomms/2015/151116/ncomms9912/extref/ncomms9912-s1.pdf

Padre Organtino
11-16-2015, 07:20 PM
Kharia do have an East Asian admixture, don't they?

IMO, it's becoming more and more clear that there were:

1.Migration of Teal farmers/gatherers

2.Aryan invaders

into India at different time frames. However, there might also be other weird layers of ancestry - I'm just pointing at the two most important so far.

Kale
11-16-2015, 07:23 PM
Figure 1 is pretty interesting...

Sharing between ancients (Ust,K14,MA1)....
Kotias - 119,137,145
Satsurblia - 122,137,143
No major difference there, but...
Bichon - 130,159,157
Very different...

The two Georgians have lower affinity to Ust-Ishim, and as such, contain something more divergent (Basal Eurasian likely suspect).

They also share a lot more with K14 and MA1 than they do with Ust-Ishim, just as Bichon, our new WHG...suggesting a sizeable West Eurasian component (maybe 60%). But unlike Bichon, they share more with MA1 than K14. So...Either the Georgian's shared some deep drift with MA1 for a short time some 40,000 or so years ago, or some post K14 interaction with MA1, or both?

Awale
11-16-2015, 08:13 PM
...Also is there a READABLE version of the admixture graph from this paper anywhere?

Been rummaging through this thread so far hoping someone would share one... Really hoping these chaps put Horners into this admixture graph.

Krefter
11-16-2015, 08:32 PM
ENF=Farmer. Is dead.

I'm not surprised by the results. It didn't make sense to me Basal Eurasians expanded only with farming. I knew Hunter gatherers of West Asia also had Basal Eurasian. West Asian genetic origins are a lot more complicated than early farmers repopulating the region.

Modern Caucasus look like they might be 50%+ from Upper Paleolithic Caucasus people. The West Asians here are probably happy with the results, they have ancestry from their region from before the Sumerians, way back in very primitive times.

The first farmers of Europe certainly had a lot of Near Eastern hunter gatherer ancestry, which clearly was closely related to hunter gatherers in Europe.

These CHG genomes fit better as Yamnaya's non-EHG ancestors than any moderns. They score almost 100% in "Teal" of the paper's ADMIXTURE. It really looks like they were the Teal people.

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

I've added Hirisplex results of the CHG genomes and new Late Upper Palaeilthic WHG genome to Pre-Historic West Eurasian Phenotype (https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1798287387).

The oldest Caucasus genome(13,300yo) and Swiss genome(13,700yo) had rs12913832 AG, confirming blue eyes are over 13,000 years old. The Swiss genome is our first Brown eyed WHG person.

Both Caucasus genomes and new WHG had CC in rs16891982. The oldest example of derived alleles in that SNP are from Sweden and Anatolia dating to 6000 BC. The new WHG had GG in rs1426654 but both Caucasus guys had AA in rs1426654. Both were Caucasus guys were confirmed to have the C11 haplotype found in 97% of AA rs1426654 today. So, far all pre-Neolithic West Eurasians are mostly derived in rs1426654, except WHG.

With these new data it appears: There was eye-color variation in both West Asia and Europe over 13,000 years ago. Blue eyes probably originated before the LGM. Caucasus had the same pigmentation-related alleles as modern West Asians. Mutations associated with Light skin existed over 13,000 years ago in at least the Caucasus(but certainly elsewhere).

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

This paper tells a lot about origins of South Asians. I'm going to post about it later. Many methods show CHG is the best proxy for non-Eastern ancestors of South Asians. They're basically the Teal, ASI, Wet Asian, signal we've seen for years. They contributed ancestry to all West Eurasians and South Asians, and probably others.

Michał
11-16-2015, 08:57 PM
What do you guys think about the lack of an ANE (MA1) affinity in the paper?

If I am not mistaken, this actually means that the "fourth ancestral tribe of the Europeans" has not been discovered yet, as CHG is only one of the four "grandparents" of Khvalynsk/Yamna. The crucial question is when and where CHG met ANE to form the "mating partner" for EHG. It could have happened in the North Caucasian region, as suggested by Generalissimo and many others. However, it seems too early to exclude an alternative scenario in which the ANE+CHG hybrid was created in the SE Caspian region where the ANE-rich population from Central Asia met the CHG-rich Early Farmer grouping originating from the South Caucasus. Whichever of those two scenarios turns correct, it seems to me that the dominant Y-DNA haplogroup of that ANE+CHG population was kind of R1, most likely R1b, or at least I cannot see any better candidate. In such case, one would need to assume that the "absence" (or very small amount) of CHG in the two known pre-Yamna R1b samples (from Samara and Khvalynsk) could have been a result of insufficient sampling and/or an extremely strong EHG admixture in the westernmost R1b groupings (or, more correctly, a relatively small autosomal "R1b-derived" admixture in the R1a-rich EHG population).

@Generalissimo
I know the exact relationship between WHG, EHG and ANE has been a matter of strong controversy, but could you please let me know what is your opinion on this question. Is the WHG+ANE=EHG formula too simplistic, and if so, what would be the more appropriate definition?

Krefter
11-16-2015, 09:42 PM
I've read through whole paper, except ADMIXTURE part it's too small to read. This is the information I've got....

Genetic continuation from Late Upper Palaeolithic-Mesolithic.
>Continuation in Georgia between 13,000-10,000yo. Continuation in Central Europe between 13,000-8,000yo.

South Asians, Yamnaya, and South Caucasus fit best as CHG+something else.
>South Asians fit best as CHG+South Indian. Yamnaya fits best as CHG+EHG. South Caucasus fits best as CHG+EF.
>D(Yoruba, X; Onge, Indian population) results say of all moderns and ancients, Indians are closest to CHG. Also, they're much closer to CHG than to Onge.

Europeans have CHG ancestry via Steppe
>Besides Caucasus, CHG shares most drift with Europeans. After that CHG shares most drift with South Asians.
>D-states and Drift(F3-stats) show European-relation to CHG follows the same pattern as Steppe ancestry. High CHG-drift first appears in Europe in Late Neolithic(we've heard the story a million times).

SouthWest Asians have CHG ancestry?
>In Supp 9. they tested f3(Target; Source1, Source2), to see what modern Eurasians fit best as an admixture of.
>SW Asians fit best as EF+African. Although Cypriots fit best as CHG+EEF. I tend to think African is hiding CHG ancestry in SW Asians, but maybe not.

CHG has complicated relationship to other Ancients(xSteppe, Steppe admixed).
>MA1 is Mr. ANE, but he very slightly closer to CHG than to EF.
>CHG is equally related to ANE and WHG(according to D-stats).
>CHG is slightly closer to EHG than to WHG.
>Of all ancients(xSteppe, Steppe admixed) CHG is closest to EF.

EF and WHG have lots of shared ancestry
>WHG, including the new 13,700 one, are much closer to EF than to CHG. Much more significantly than CHG is closer to EF than to WHG.

ZephyrousMandaru
11-16-2015, 10:14 PM
I think it's a bit premature to hastily declare the the "teal" component is real from these findings alone. We haven't yet discovered and analyzed genomes from the Middle East or South Asia. Which for all we know, night also harbor some of that teal, who might also carry older subclade variants of J.

J Man
11-16-2015, 10:15 PM
It seems, that EHGs and CHGs shared haplogroup J:

EHG, 3 samples of Y-DNA - R1b, R1a, J
CHG, 2 samples of Y-DNA - J, J2

Yes they did. This is getting really interesting!

J Man
11-16-2015, 10:20 PM
They are indeed. The results are now up in my online tables:
http://www.ancestraljourneys.org/palaeolithicdna.shtml
http://www.ancestraljourneys.org/mesolithicdna.shtml

There seems to have been a bit of a mix up when it comes to reporting the Y-DNA haplogroups of these CHG samples. In the paper itself it says.

''Continuity in the Caucasus is also supported by the mitochondrial and Y chromosomal haplogroups of Kotias (H13c and J2a, respectively) and Satsurblia (K3 and J), which are all found at high frequencies in Georgia today22, 23, 24 (Supplementary Note 8).''

But in the Supplementary Note 8 link it says.

http://www.nature.com/ncomms/2015/151116/ncomms9912/extref/ncomms9912-s1.pdf

''Supplementary Table 19. Y chromosome haplogroups for ancient male samples.
Sample Major haplogroup Maximum likelihood haplogroup Confidence haplogroup
Kotias J J J
Satsurblia J J2a J2
Bichon I I2a* I2
Haplogroups were determined by Yfitter13. The “maximum likelihood haplogroup” is described by 13, as being the best guess
haplogroup while the “confidence haplogroup” is described as the conservative guess haplogroup.''


Below this again in the Supplementary Note 8 link it says.

''Y-chromosomal haplogroups
Both Georgian hunter-gatherer samples were assigned to haplogroup J with Kotias belonging to
the subhaplogroup J2a (see methods). Haplogroup J is estimated to have arisen 31.7 kya in the
Middle East and is widely distributed in Eurasia, the Middle East and North Africa48,49. Patterns
of haplogroup frequency are consistent with an expansion from the Middle East towards Europe
which has been suggested to have accompanied the Neolithic transition in Europe48,50,51. In a
study exploring J haplogroups in 445 individuals from Eurasia, J2a was found at highest
frequency in Georgia and Iraq48. It is intriguing that both the mitochondrial and Y chromosome
haplogroups of our ancient Georgian samples have been associated with the Neolithization of
Europe. This tentatively suggests a genetic link between Georgian hunter-gatherers and early
European migrants from the Near East.''



So which is correct I wonder? Is Kotias J or J2a? Is Satsurblia J or J2a?

MfA
11-16-2015, 10:27 PM
I tend to agree with Matt @Eurogenes, ANE will dramatically decline in west Asia and only a few population will score double digits. South-central Asians won't score it as much as Karitianans either. http://eurogenes.blogspot.com/2015/11/fourth-strand-of-european-ancestry.html?showComment=1447703965425#c388348819 7688505116

ADW_1981
11-16-2015, 10:37 PM
If I am not mistaken, this actually means that the "fourth ancestral tribe of the Europeans" has not been discovered yet, as CHG is only one of the four "grandparents" of Khvalynsk/Yamna.

If I remember correctly, Khvalynsk was quite a bit earlier than Yamnaya and showed only a small amount of CHG, similar to the EHG Samara reference which shows about the same. By the time Yamnaya rolls around, the CHG input is much larger.

Tag Heuer
11-16-2015, 10:59 PM
that explains high Chechen/Caucasian admix among Indo-Iranians.

Gravetto-Danubian
11-16-2015, 11:10 PM
EHG, CHG and AEF (Anatolian Early Farmers) autosomal groups and their Y-DNA:

Unfortunately vast areas still remain completely unsampled for ancient DNA.

http://s17.postimg.org/y4i4vf4bj/EHG_CHG_AEF.png

What's an "early Anatolian Farmer" ? I don't think its an actual population.

During the LGM, Anatolia was probably populated (sparsely) by WHG-like I2 groups (around Marmara, and Antalya), and CHG like J groups (to the east). G2 etc came later with the early Neolithic. So your AEF is a later composite, not a LGM isolate clade.

Gravetto-Danubian
11-16-2015, 11:13 PM
Here is a previous paper (from 2014) with the same samples from the same sites in Georgia:

"Satsurblia: New Insights of Human Response and Survival across the Last Glacial Maximum in the Southern Caucasus":

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111271


According to this paper, the south Caucaus wasn't actually populated between 25- 18 kya ie the peak of the LGM.

This means, these CHG/ J2 groups had to arrive from elsewhere ?! (Im guessing somewhat more south)

jeanL
11-16-2015, 11:42 PM
Here is a couple of figures and table of interest to me.

Figure-S3
6639

Notice that the Basques but not the Spanish(North) or French South samples has equally high shared drift with the Bichon(Funny thing, Bichon means big bug in Spanish) sample compared to Northern European samples. On other hand the shared drift with Kotias is lowest in Sicilians and Maltese, followed by Basques, French South, Spanish, Sardinians and North Italians.

Here is table-S9:

6640

Only the Basque and Sardinians get LBK+Bichon as their lowest f3 stats, all other Europeans get other Hunter Gatherers. See the table zoomed-in:

6641

Notice that Spanish(North) and French South both the closest samples to Basques get Scandinavian HG instead of Bichon. They also get Hungary_EN instead of LBK. Notice also that all other Southern Europeans get Samara_HG or even MA1, does this have to do with Sardinians followed by Basques having the lowest ANE in Europe? Another interesting group is Estonians that get Kotias and Loschbour as their lowest f3 score, whereas Finns and Lithuanians just get Hungary_EN+Samara_HG. How about the Scottish? Loschbour+Iraqi_Jew, interesting?

Thoughts?

Michał
11-16-2015, 11:48 PM
If I remember correctly, Khvalynsk was quite a bit earlier than Yamnaya and showed only a small amount of CHG, similar to the EHG Samara reference which shows about the same. By the time Yamnaya rolls around, the CHG input is much larger.
The "teal" component (and thus presumably also CHG) was significantly stronger in Khvalynsk than in the earlier EHG-rich samples (ie. in the Karelian R1a and Early Samara R1b samples), yet not evenly distributed in all three Khvalynsk males (R1b>R1a>Q), so Khvalynsk was likely a population where EHG first met ANE+CHG and where all those components eventually merged. My point is that the parental ANE+CHG (and non-EHG?) population that contributed to Khvalynsk (and thus to the descending Yamna and Corded Ware cultures) was quite likely to be R1-rich, as it is hard to imagine any other Y-DNA haplogroup that would correspond to the ANE part in such Caucasian/Caspian ANE+CHG mix, especially when assuming that this population was ancestral to Khvalynsk, Yamna and Corded Ware. So either that unknown R1 (R1b?) Y-DNA steppe component was lost at some point (and replaced by J2, due to genetic drift or for any other reason) and it was only the ANE+CHG females who contributed to Khvalynsk, or, alternatively, it was haplogroup R1b (R1b-M269?) that was associated first with a non-EHG ANE-rich population that merged with CHG and then with the resulting ANE+CHG population that merged with EHG. If the latter scenario is correct, then the autosomal composition of the only known pre-Khvalynsk Eastern European R1b (M269-) sample should be considered to be either an EHG-admixed "outlier" or a very distant relative of the major early R1b (CHG-admixed) group.

alan
11-16-2015, 11:53 PM
I dont really find this all that surprising. After all everyone was a hunter until a certain point in time. Even farmers are ultimately an economic development among epipalaeolithic hunters in northern Mesopotamia. Other hunters in south-west Asia simply remained out of the loop of this development for a long period. Recall that the Caucasus was late to farming, as was northern Iran east of the Zagros and the east Caspian. Several different hunter groups would have been strung along that zone before farming spread. Once they acquired farming they would have undergone a secondary expansion. The big question is how far east did the CHG signal go?

Well archaeology can probably infer that. If you read about upper and epi palaeolithic archaeology in the Caucasus the Caucasian Gravettian roots keep jumping out at you. So it seems to stand to reason that the same genetic signal wont exist east of this non-European part of the Gravettian spread. I found a paper showing Armenia had a Gravettian derived upper and epipalaeolithic too
http://www.digitorient.com/wp/wp-content/uploads/2013/09/Montoya-et-al.-2013-JHE-in-press.pdf

Gravetto-Danubian
11-17-2015, 12:06 AM
The "teal" component (and thus presumably also CHG) was significantly stronger in Khvalynsk than in the earlier EHG-rich samples (ie. in the Karelian R1a and Early Samara R1b samples), yet not evenly distributed in all three Khvalynsk males (R1b>R1a>Q), so Khvalynsk was likely a population where EHG first met ANE+CHG and where all those components eventually merged. My point is that the parental ANE+CHG (and non-EHG?) population that contributed to Khvalynsk (and thus to the descending Yamna and Corded Ware cultures) was quite likely to be R1-rich, as it is hard to imagine any other Y-DNA haplogroup that would correspond to the ANE part in such Caucasian/Caspian ANE+CHG mix, especially when assuming that this population was ancestral to Khvalynsk, Yamna and Corded Ware. So either that unknown R1 (R1b?) Y-DNA steppe component was lost at some point (and replaced by J2, due to genetic drift or for any other reason) and it was only the ANE+CHG females who contributed to Khvalynsk, or, alternatively, it was haplogroup R1b (R1b-M269?) that was associated first with a non-EHG ANE-rich population that merged with CHG and then with the resulting ANE+CHG population that merged with EHG. If the latter scenario is correct, then the autosomal composition of the only known pre-Khvalynsk Eastern European R1b (M269-) sample should be considered to be either an EHG-admixed "outlier" or a very distant relative of the major early R1b (CHG-admixed) group.

Agree with everything, except I'dlike to clarify two things:

1) can you re-clarify what you're suggesting ? :)

2) I don't think Khvalynsk was the earliest mixing point. Id put it at where the Kuban region opens up unto the steppe, i.e. at the incipient areas of 'steppe Majkop' and Konstantinovka culture area. Khvalynsk is further north (approaching the middle Volga), and IMO, more peripheral to the whole affair.

alan
11-17-2015, 12:25 AM
The "teal" component (and thus presumably also CHG) was significantly stronger in Khvalynsk than in the earlier EHG-rich samples (ie. in the Karelian R1a and Early Samara R1b samples), yet not evenly distributed in all three Khvalynsk males (R1b>R1a>Q), so Khvalynsk was likely a population where EHG first met ANE+CHG and where all those components eventually merged. My point is that the parental ANE+CHG (and non-EHG?) population that contributed to Khvalynsk (and thus to the descending Yamna and Corded Ware cultures) was quite likely to be R1-rich, as it is hard to imagine any other Y-DNA haplogroup that would correspond to the ANE part in such Caucasian/Caspian ANE+CHG mix, especially when assuming that this population was ancestral to Khvalynsk, Yamna and Corded Ware. So either that unknown R1 (R1b?) Y-DNA steppe component was lost at some point (and replaced by J2, due to genetic drift or for any other reason) and it was only the ANE+CHG females who contributed to Khvalynsk, or, alternatively, it was haplogroup R1b (R1b-M269?) that was associated first with a non-EHG ANE-rich population that merged with CHG and then with the resulting ANE+CHG population that merged with EHG. If the latter scenario is correct, then the autosomal composition of the only known pre-Khvalynsk Eastern European R1b (M269-) sample should be considered to be either an EHG-admixed "outlier" or a very distant relative of the major early R1b (CHG-admixed) group.

I still believe that EHG itself is a composite of a WHG type population and a new influx of ANE in the early Mesolithic. So in other words ANE was an independent wave and would only form EHG where it mixed with WHG-like populations. That would explain why it is possible to have ANE rich populations lacking the other components in EHG i.e ANE could mix with any group it encountered. I very strongly suspect that when pre-younger Dryas eastern European hunters are tested they will lack the ANE component.

Krefter
11-17-2015, 12:27 AM
I think it's a bit premature to hastily declare the the "teal" component is real from these findings alone. We haven't yet discovered and analyzed genomes from the Middle East or South Asia. Which for all we know, night also harbor some of that teal, who might also carry older subclade variants of J.

Several tests proved CHG is the best proxy for the non-EHG side of Yamnaya aka Teal. So, they're in fact our best representative for Teal.


I tend to agree with Matt @Eurogenes, ANE will dramatically decline in west Asia and only a few population will score double digits. South-central Asians won't score it as much as Karitianans either. http://eurogenes.blogspot.com/2015/11/fourth-strand-of-european-ancestry.html?showComment=1447703965425#c388348819 7688505116

CHG has lots of ANE. ANE is not well defined. MA1 is so old that the new Caucasus DNA doesn't have a very close relationship to it.

Gravetto-Danubian
11-17-2015, 12:30 AM
I still believe that EHG itself is a composite of a WHG type population and a new influx of ANE in the early Mesolithic. So in other words ANE was an independent wave and would only form EHG where it mixed with WHG-like populations. That would explain why it is possible to have ANE rich populations lacking the other components in EHG i.e ANE could mix with any group it encountered. I very strongly suspect that when pre-younger Dryas eastern European hunters are tested they will lack the ANE component.

I wouldn't disagree on that.
AFAIK, Pinhasi tested more than just these EpiPalaeolithic and Mesolithic samples. Johaness Krause tested others still.
I hope when their further data comes out it'll all be crystal clear

Michał
11-17-2015, 01:31 AM
1) can you re-clarify what you're suggesting ? :)
:) Yes, I agree that 1) it is quite complicated and 2) my post wasn't clear enough.

I forgot to mention one important thing, namely that we know for sure that the Caucasian/Southern component (now known to correspond to CHG) was "not alone" when it was somehow introduced to the EHG (R1-rich) steppe population. In other words, that source population was rich in both CHG and ANE, with the ANE levels equal to those present in EHG.

Let's assume for a moment that EHG could be considered a mixture of ANE and WHG (though I am not sure if this is a good approximation). In such case, Yamna (and probably the closely related cultures like Sredny Stog and Late Khvalynsk) arose as a consequence of an important merging process that started no later than Early Khvalynsk and was completed by the Yamna period). The two merging populations were the Eastern European population rich in WHG and ANE (or the EHG population, as represented by the Karelian R1a and Early Samara R1b samples) and an unknown "Southern" population that was rich in ANE and CHG. This means that both these ancestral populations included significant levels of ANE, yet these two ANE components (let's call them ANE1 and ANE2) have been separated from each other long time ago. We know that ANE1 in EHG was likely associated with haplogroup R1, so the major questions are:
1) When and how did the ANE2+CHG population arise? Where was it located?
2) What were the Y-DNA haplogroups associated with ANE2 and ANE2+CHG?
3) If ANE2 and ANE2+CHG were associated with haplogroup R1 (R1b) then which subclades of R1 (R1b) were associated with ANE1 and ANE2, respectively?
4) What is the likelihood that EHG (or ANE1+WHG) was associated mostly with R1a, so that the EHG sample from Samara (R1b M269-) was only an "outlier" who did not contribute to the further development of any major steppe or forest-steppe culture?



2) I don't think Khvalynsk was the earliest mixing point. Id put it at where the Kuban region opens up unto the steppe, i.e. at the incipient areas of 'steppe Majkop' and Konstantinovka culture area. Khvalynsk is further north (approaching the middle Volga), and IMO, more peripheral to the whole affair.
When I mentioned Khvalynsk I meant the entire territory covered by this large culture, and I agree that some earliest mixing points could have been located further south than Khvalynsk itself. The exact location of that first encounter would of course depend on where the mysterious population rich in both ANE and CHG was located.

Jean M
11-17-2015, 02:00 AM
... we know for sure that the Caucasian/Southern component (now known to correspond to CHG) was "not alone" when it was somehow introduced to the EHG (R1-rich) steppe population. In other words, that source population was rich in both CHG and ANE, with the ANE levels equal to those present in EHG.

Do we really know this? It seems to have been an assumption simply from the fact that Yamnaya samples were higher in ANE than the very small number of EHG samples. That could easily be the result of a smallish band of ANE-rich men arriving initially in the Samara region from Siberia, and some subsequent intermarriage with locals diluting the ANE level, followed by more ANE-rich arrivals from Siberia boosting the ANE level. The ANE does not have to be linked to the CHG input.

Gravetto-Danubian
11-17-2015, 02:14 AM
:) Yes, I agree that 1) it is quite complicated and 2) my post wasn't clear enough.

I forgot to mention one important thing, namely that we know for sure that the Caucasian/Southern component (now known to correspond to CHG) was "not alone" when it was somehow introduced to the EHG (R1-rich) steppe population. In other words, that source population was rich in both CHG and ANE, with the ANE levels equal to those present in EHG.

Let's assume for a moment that EHG could be considered a mixture of ANE and WHG (though I am not sure if this is a good approximation). In such case, Yamna (and probably the closely related cultures like Sredny Stog and Late Khvalynsk) arose as a consequence of an important merging process that started no later than Early Khvalynsk and was completed by the Yamna period). The two merging populations were the Eastern European population rich in WHG and ANE (or the EHG population, as represented by the Karelian R1a and Early Samara R1b samples) and an unknown "Southern" population that was rich in ANE and CHG. This means that both these ancestral populations included significant levels of ANE, yet these two ANE components (let's call them ANE1 and ANE2) have been separated from each other long time ago. We know that ANE1 in EHG was likely associated with haplogroup R1, so the major questions are:
1) When and how did the ANE2+CHG population arise? Where was it located?
2) What were the Y-DNA haplogroups associated with ANE2 and ANE2+CHG?
3) If ANE2 and ANE2+CHG were associated with haplogroup R1 (R1b) then which subclades of R1 (R1b) were associated with ANE1 and ANE2, respectively?
4) What is the likelihood that EHG (or ANE1+WHG) was associated mostly with R1a, so that the EHG sample from Samara (R1b M269-) was only an "outlier" who did not contribute to the further development of any major steppe or forest-steppe culture?
.

I have wondered the very same thing - that R1a is the "native" EHG and R1b is more southeastern; but these Caucasus samples lacked any R1. Of course more samples from Central Asia might change that.

Also - and I'm still digesting this new data- I thought the study concluded that these Caucasus hunters didn't actually have ANE, and CHG isnt actually related to ANE , but it only behaved as if it were ANE + EF due to the limitations and errors of qp-admin and admixture (?)

In fact, they explicitly state that "Teal" - now "CHG"- is more closely related to Basal Eurasian, but split off c. 22 kya.

Chad Rohlfsen
11-17-2015, 02:19 AM
Once again, for what feels like the hundredth time on here; teal is not a real population, nor does it represent this population. When Yamnaya was 50% teal, the other half was Euro HG, which was Motala. Yamnaya is not 50% Motala, therefore, CHG is not teal. Teal is an artificial construct of Admixture. Seriously, how many times does it have to be explained? Also, ANE is out of the conversation at this point. Mal'ta may not be anymore important than Kostenki.

Michał
11-17-2015, 02:23 AM
Do we really know this? It seems to have been an assumption simply from the fact that Yamnaya samples were higher in ANE than the very small number of EHG samples. That could easily be the result of a smallish band of ANE-rich men arriving initially in the Samara region from Siberia, and some subsequent intermarriage with locals diluting the ANE level, followed by more ANE-rich arrivals from Siberia boosting the ANE level. The ANE does not have to be linked to the CHG input.
How would you date this hypothetical second wave out of Siberia? Did this smallish (and I guess relatively late) band of people have enough time to nearly double the level of ANE among the local majority (so ANE could reach the previous level after intensive mixing with CHG)?

J Man
11-17-2015, 02:33 AM
What's an "early Anatolian Farmer" ? I don't think its an actual population.

During the LGM, Anatolia was probably populated (sparsely) by WHG-like I2 groups (around Marmara, and Antalya), and CHG like J groups (to the east). G2 etc came later with the early Neolithic. So your AEF is a later composite, not a LGM isolate clade.

You very well could be right about this.

Krefter
11-17-2015, 02:36 AM
1) When and how did the ANE2+CHG population arise? Where was it located?


CHG had lots of "ANE". MA1 is so old that everyone is more related to samples from 8,000 or whatever years ago than MA1. CHG literally scores almost 100% in a new Teal component in ADMIXTURE. Yamnaya is a two-way mixture in ADMIXTURE of the new Teal and HG-centered component. Yamnaya shares more drift with CHG than with any West Asian pops who were used as Yamnaya's proxy West Asian ancestor. CHG fits better as ASI than any modern pops, it's very likely that's where South Asians get a lot of their ANE. South Caucasus posp fit best as EEF+CHG. They got their ANE from CHG.


Once again, for what feels like the hundredth time on here; teal is not a real population, nor does it represent this population. When Yamnaya was 50% teal, the other half was Euro HG, which was Motala. Yamnaya is not 50% Motala, therefore, CHG is not teal. Teal is an artificial construct of Admixture. Seriously, how many times does it have to be explained? Also, ANE is out of the conversation at this point. Mal'ta may not be anymore important than Kostenki.


Sure, Teal exactly as ADMIXTURE has it didn't exist. However a very similar population did and that's who CHG is. The Teal signal that has been detected for years is a very real type of ancestry that doesn't exactly represent the ancient people who are the source but is very close.

J Man
11-17-2015, 02:43 AM
Well they were hunters in the Palaeolithic, yes. By the Copper Age, the south Caucasus had a very diverse economy consisting of both Pastoral and farming elements. People often erroneously think anything south of the caucuses is automatically and exclusively "farming". This is incorrect

This population then moved to the north caucuses circa 4200 BC – the start of the pre-Majkop phase, and then gradually mixed with the EHG groups between 4000-3000 BC.

I think that what this paper shows is that even after Neolithic farming had first developed further South in the Levant area there were already Y-DNA haplogroup J and J2 hunter-gatherer populations in the Caucasus that were still technologically and economically Mesolithic. Maybe these Y-DNA haplogroup J and J2 populations received agriculture after the earliest Neolithic farmers migrated North out of the Levant?

Chad Rohlfsen
11-17-2015, 03:25 AM
CHG had lots of "ANE". MA1 is so old that everyone is more related to samples from 8,000 or whatever years ago than MA1. CHG literally scores almost 100% in a new Teal component in ADMIXTURE. Yamnaya is a two-way mixture in ADMIXTURE of the new Teal and HG-centered component. Yamnaya shares more drift with CHG than with any West Asian pops who were used as Yamnaya's proxy West Asian ancestor. CHG fits better as ASI than any modern pops, it's very likely that's where South Asians get a lot of their ANE. South Caucasus posp fit best as EEF+CHG. They got their ANE from CHG.

What? Did you even read the paper? CHG forms clades to the exclusion of MA1, all around. It's not close to MA1. Please, read the paper.

Krefter
11-17-2015, 03:28 AM
The ADMIXTURE results are impossible to read in Supp info. But the paper gives a good description of the results in Supp. Note 9. In Summary what they say is...


>A Middle Eastern component appears in K=9.
>From K=9-K=15 CHG is a mixture of it and a South Asian centered component.
>The South Asian component first appears in late Neolithic Europeans, and today most Europeans and West Asians have membership in it. The rest of West Eurasians score in SHG/EHG/WHG centered component and Middle Eastern component.


In K=15 the older CHG scores 100% in a new Caucasus-centered component but the younger one scores just under 10% in a Middle Eastern component. Caucasus today score almost 50% in Middle Eastern component and over 50% in CHG. From K=15-K=20 nothing really changes.
South Asians are a mixture of CHG component and another South Asian component.


>Europeans are mostly a mixture of SHG/WHG/EHG+CHG+MIddle Eastern. West Asians are mostly a mixture of CHG+Middle Eastern.


>By K=18 it looks like Middle Easterns splits into typical Mediterranean and SW Asian.

Krefter
11-17-2015, 03:29 AM
What? Did you even read the paper? CHG forms clades to the exclusion of MA1, all around. It's not close to MA1. Please, read the paper.

That doesn't matter because MA1 is old. Everything else in the paper is screaming "Most ASI and Teal is CHG!!".

Kurd
11-17-2015, 03:29 AM
This is what I posted a few days ago at http://www.anthrogenica.com/showthread.php?5591-Post-Eurasia-14-Ancient-Modern-Oracles/page9

ADMIXTURE does not tell us the direction of gene flow. For some, Yamnaya represents actual direct gene flow from a Yamnaya type population, whereas for others, perhaps like yourself, Yamnaya represents their/your shared ancestry with a population that contributed to the creation of Yamnaya types. I believe that populations similar to BA Armenians ( which are different from modern Armenians) in combination with Eastern Hunter Gatherer types contributed to the creation of Yamanya type

parasar
11-17-2015, 03:31 AM
Several tests proved CHG is the best proxy for the non-EHG side of Yamnaya aka Teal. So, they're in fact our best representative for Teal.
...
CHG has lots of ANE. ANE is not well defined. MA1 is so old that the new Caucasus DNA doesn't have a very close relationship to it.

AG2 and MA1 are not that different in their makeup and are 7000 years apart.
Nor are Satsurblia and Kotias that different and they are ~4000 years apart.
And Satsurblia is Upper Paleolithic.

So age of MA1 does not seem to be an issue at all.

"MA1 and CHG plot in distinct regions of the PCA and also have very different profiles in the ADMIXTURE analysis (Fig. 1). Second, when we test if CHG shows any evidence of excess allele sharing with MA1 relative to WHG using tests of the form D(Yoruba, CHG; MA1, WHG) no combinations were significantly positive... All northern Europeans showed a significant sharing of alleles with MA1 separate to any they shared with CHG."

J Man
11-17-2015, 03:31 AM
Yes according to this paper the CHG population/clade separated from the WHG population/clade around 45,000 years ago and then later separated from the ancestors of the Neolithic farmers (EEF/ENF?) around 25,000 years ago. It sounds like CHG is a distinct clade unto itself.

Tag Heuer
11-17-2015, 03:46 AM
ANE7 and K36 calculator results (on Upper Palaeolithic genome from Satsurblia cave, Georgia):


7 ancestral populations
229157 total SNPs
100 flipped SNPs
99 heterozygous SNPs
0 no-calls
193419 absent SNPs
0.155954 genotype rate
mode genomewide

193419 SNPs missing (no-call or absent)
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

23.62% ANE
0.52% ASE
9.65% WHG-UHG
0.00% East_Eurasian
3.12% West_African
0.70% East_African
62.40% ENF



36 ancestral populations
165688 total SNPs
9 flipped SNPs
70 heterozygous SNPs
0 no-calls
139614 absent SNPs
0.157368 genotype rate
mode genomewide

139614 SNPs missing (no-call or absent)
----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

0.00% Amerindian
0.00% Arabian
17.43% Armenian
0.00% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
0.00% East_Central_Euro
0.01% East_Med
0.00% Eastern_Euro
0.00% Fennoscandian
0.00% French
0.00% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
0.00% North_Atlantic
46.99% North_Caucasian
0.00% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
4.00% West_African
31.57% West_Caucasian
0.00% West_Med

Krefter
11-17-2015, 03:54 AM
ADMIXTURE proves CHG had what we call ANE. parasar MA1 is more related to Northern Europeans because they have less Basal Eurasian than CHG does. Same reason MA1 is closesr to WHG compared modern people.

parasar
11-17-2015, 04:07 AM
ADMIXTURE proves CHG had what we call ANE. parasar MA1 is more related to Northern Europeans because they have less Basal Eurasian than CHG does. Same reason MA1 is closesr to WHG compared modern people.

First, ADMIXTURE should not be used since it will not distinguish between ancestral sharing vs. real admixture.
Second, we have to look at allele sharing, and the alleles northern Europeans share with MA1 are not the same ones they share with CHG, it is not a matter of less or more.

On another separate point, much like WHG these CHG do not look like that robust a population to me. So I would not be surprised if the actual admixture into Yamna came from a CHG related population rather than CHG.

Chad Rohlfsen
11-17-2015, 04:08 AM
It's being forced to fit clusters. It will pick what best describes it, not necessarily true. Just as EHG can be modeled as Loschbour+SC Asian+Karitiana. That is what it does. It finds best fits. Look at the stats. It isn't close to MA1 at all. You need to understand how these tests and Admixture work, and how to read stats. If anything, this might hint that HG in CHG could be largely undifferentiated West Eurasian, equally related to WHG and ANE, but not descended from either one, rather ancestral to both.

Krefter
11-17-2015, 04:18 AM
First, ADMIXTURE should not be used since it will not distinguish between ancestral sharing vs. real admixture.
Second, we have to look at allele sharing, and the alleles northern Europeans share with MA1 are not the same ones they share with CHG, it is not a matter of less or more.

On another separate point, much like WHG these CHG do not look like that robust a population to me. So I would not be surprised if the actual admixture into Yamna came from a CHG related population rather than CHG.

Davidski's ANE component is made up of MA1 or the non-East Asian side of Native Americans, I don't know which. Anyways, it's not madeup of Caucasus people or anyone with CHG-related stuff, so CHG must have MA1 related ancestry. Where did you see that MA1 shares specific alleles with North Europeans that he doesn't with CHG? And if he does it could be just CHG has Basal Eurasian alleles where North Europeans have ANE/WHG alleles. CHG looks robust to me, they both share almost as much drift with each other as La Brana 1 and Loschbour do with each other.

ZephyrousMandaru
11-17-2015, 04:23 AM
Several tests proved CHG is the best proxy for the non-EHG side of Yamnaya aka Teal. So, they're in fact our best representative for Teal.

Is this for teal in the Yamnaya or for the teal component in general as it is represented in all modern populations?

Chad Rohlfsen
11-17-2015, 04:28 AM
Davidski's ANE component is made up of MA1 or the non-East Asian side of Native Americans, I don't know which. Anyways, it's not madeup of Caucasus people or anyone with CHG-related stuff, so CHG must have MA1 related ancestry. Where did you see that MA1 shares specific alleles with North Europeans that he doesn't with CHG? And if he does it could be just CHG has Basal Eurasian alleles where North Europeans have ANE/WHG alleles. CHG looks robust to me, they both share almost as much drift with each other as La Brana 1 and Loschbour do with each other.

You don't understand how these tests and Admixture work. Sorry, but you're way off here. You're not understanding the paper either.

parasar
11-17-2015, 04:33 AM
Davidski's ANE component is made up of MA1 or the non-East Asian side of Native Americans, I don't know which. Anyways, it's not madeup of Caucasus people or anyone with CHG-related stuff, so CHG must have MA1 related ancestry. Where did you see that MA1 shares specific alleles with North Europeans that he doesn't with CHG? And if he does it could be just CHG has Basal Eurasian alleles where North Europeans have ANE/WHG alleles. CHG looks robust to me, they both share almost as much drift with each other as La Brana 1 and Loschbour do with each other.

I was not clear. By robust I was not referring to the component but the population. "WHG and CHG who display an excess of shorter ROH, akin to modern Oceanic and Onge populations, and EF who resemble other populations with sustained larger ancestral population sizes."

Chad Rohlfsen
11-17-2015, 04:35 AM
I'm staking my money on a largely undifferentiated west eurasian with "BE".

Krefter
11-17-2015, 04:46 AM
Is this for teal in the Yamnaya or for the teal component in general as it is represented in all modern populations?

Drift stats. Yamnaya shares more drift with CHG than with any modern West Asians. CHG also represents as pure Teal in ADMIXTURE. Yamnaya fits as a mix of CHG and EHG/WHG/SHG.


You don't understand how these tests and Admixture work. Sorry, but you're way off here. You're not understanding the paper either.

I took a lot of notes. Supp. Table 8 is what claims CHG and EF form a clade as opposed to MA1. Although the stats show MA1 is slightly closer to CHG. Also, CHG is closer to EHG than to WHG in D-stats. Add to that MA1 is slightly closer to WHG than to CHG in D-stats. D-stats aren't very precise. I've seen crazy results, like Sephedric Jews being closer to English than Sicilians.
MA1; Kotias Stuttgart -0.0153
MA1; Kotias NE1 -0.0083

Gravetto-Danubian
11-17-2015, 04:51 AM
I'm staking my money on a largely undifferentiated west eurasian with "BE".

Chad can you specify & detail what exactly you're seeing between all the different basal groups (BE, ANE, whg, CHG, EHG) (sorry if you're repeating yourself).

vettor
11-17-2015, 05:17 AM
some of you guys are failing to "see the wood for the trees" as van Oven puts it
https://en.wikipedia.org/wiki/Paragroup

I and J findings from this paper was early, pre any R1 by a looonnng time.............actually only G , L, T where around ...............R1 was still under the K2 band
Karafet estimates the IJ split at 22000 ............surely for I to get to Switzerland was not in any great speed from outside of Europe ...or....was IJ still in union in Europe!

Krefter
11-17-2015, 05:19 AM
@Chad and parasar,

I just remembered. In D-stats MA1 is not significantly closer to Georgians as to Sardinians.

Ju_hoan_North MA1 BedouinB Sardinian 0.0349
Ju_hoan_North MA1 BedouinB Georgian 0.0411

Jean M
11-17-2015, 05:25 AM
How would you date this hypothetical second wave out of Siberia? Did this smallish (and I guess relatively late) band of people have enough time to nearly double the level of ANE among the local majority (so ANE could reach the previous level after intensive mixing with CHG)?

I suspect that some ANE arrived with pressure blade making, and more with the earliest pottery. The latter was clearly the big clue that led David Anthony to propose looking at the Samara samples he had. But we would be led astray I think to picture waves of arrivals as though these were large populations who turned up all at once. They were hunter-gatherers, who travelled in small bands. New bands could turn up. Bands could come and go.

For that matter they could move across the Caspian and most probably did, since we have what seems to be their blades in both areas and the etchings of boats beside the Caspian. So it is not inconceivable that some mixed with the local hunter-gatherers of the Caucasus to produce a mixed population, some of whom were absorbed into the steppe over the millennia, not necessarily in one swoop, but more as a trickle over time. I have no desperate desire to deny that possibility. I just feel we are best not to assume too much at this stage.

Arame
11-17-2015, 07:41 AM
I remember Dienekes posting that Armenians and Georgians don't have ANE.

http://dienekes.blogspot.am/2015/03/two-observations-on-ancestry-of.html

My friend from an Armenian group was also claiming that ANE is very low in Armenians. But I didn't believe that.
Experts of autosomes what is Your opinion on this now ?
I mean ANE outside CHG not inside it.

DMXX
11-17-2015, 08:13 AM
^ I agree with Chad. Mal'ta and the ANE component lose meaning the closer towards the present our aDNA roster becomes.

Both EHG and CHG likely have "ANE" embedded within them (evidence of this is clearer with EHG). Relegating Mal'ta and ANE to a vestigial position is fast becoming our reality the more samples we get from West Eurasia's mesolithic and neolithic. In light of CHG's conceptualisation, I suppose an independent ANE component (representing "surplus" amounts) would only be relevant for South-Central Asians and South Asians. But it may not be. A combination of EHG and CHG could very well account for the overwhelming majority of ANE observed in these groups.

Also, the CHG-WHG pairing in their phylogeny could explain the "West European" or "WHG" component scores observed in some of our current GEDmatch calculators for modern South/South-Central Asians.

As it stands, we only really need aDNA from Near-Eastern and South Asian HG's now to broadly reconstruct the demographic movements in West Eurasia.

Padre Organtino
11-17-2015, 08:14 AM
Of course Europeans show additional sharing with ANE beyond CHG alleles. Maybe that's because the other half of Yamnaya is basically a mix of WHG and ANE ?

Kurd
11-17-2015, 10:25 AM
I remember Dienekes posting that Armenians and Georgians don't have ANE.

http://dienekes.blogspot.am/2015/03/two-observations-on-ancestry-of.html

My friend from an Armenian group was also claiming that ANE is very low in Armenians. But I didn't believe that.
Experts of autosomes what is Your opinion on this now ?
I mean ANE outside CHG not inside it.

From a cursory overview of the paper, CHG and EF are considered sister groups (discussion and flowchart) that split from a common "BE" ancestor. ADMIXTURE, as I have previously mentioned does not convey direction of geneflow. So, if BA Armenians or CHG were to show ANE in ADMIXTURE, this does not mean that they had actual ANE (the component modal to MA1) input. The main reason BA Armenians and CHG would show ANE in ADMIXTURE, and their sister group EF would not show any, is because they have contributed to Yamnaya (something that I have suspected for a while now), and EF has not. Since Yamnaya has EHG input (ANE), this ANE would also show up in BA Armenians and CHG.

I will do some analysis as soon as I am able to incorporate those genomes into my datasets.

Kurd
11-17-2015, 10:43 AM
Of course Europeans show additional sharing with ANE beyond CHG alleles. Maybe that's because the other half of Yamnaya is basically a mix of WHG and ANE ?

ANE and WHG share more drift with each other than either does with CHG. From the steppe, Europeans received actual ANE input, CHG in steppe groups, and shared ANE/WHG ancestry. From Europe, they received actual WHG input.

" It is interesting to note that Bichon, as well as other WHG, form a clade with both MA1 and EHG to the exclusion of CHG (Supplementary Table 6). This suggests the Ancient North Eurasian (ANE) ancestry and WHG ancestry may have shallower roots and diverged subsequent to splitting from CHG (Supplementary Fig. 2). This is consistent with ADMIXTURE analysis and the geographic range of these groups -CHG were separated from these North Eurasian hunter-gatherers by the Caucasus mountain range"

Tolan
11-17-2015, 11:17 AM
ANE and WHG share more drift with each other than either does with CHG. From the steppe, Europeans received actual ANE input, CHG in steppe groups, and shared ANE/WHG ancestry. From Europe, they received actual WHG input.

" It is interesting to note that Bichon, as well as other WHG, form a clade with both MA1 and EHG to the exclusion of CHG (Supplementary Table 6). This suggests the Ancient North Eurasian (ANE) ancestry and WHG ancestry may have shallower roots and diverged subsequent to splitting from CHG (Supplementary Fig. 2). This is consistent with ADMIXTURE analysis and the geographic range of these groups -CHG were separated from these North Eurasian hunter-gatherers by the Caucasus mountain range"

6646

With this Fig 2, probably CHG has no ANE!
BA Armenian are a mixture and they are different from CHG

Tomenable
11-17-2015, 11:42 AM
Of course Europeans show additional sharing with ANE beyond CHG alleles.

That's quite obvious, after all EHGs had been a mix of WHG + ANE already before mixing with CHGs.


With this Fig 2, probably CHG has no ANE!

So ANE in Yamnaya and in modern Europe comes mostly from EHGs after all, not from "Teal people".

parasar
11-17-2015, 01:18 PM
That's quite obvious, after all EHGs had been a mix of WHG + ANE already before mixing with CHGs.



So ANE in Yamnaya and in modern Europe comes mostly from EHGs after all, not from "Teal people".

Teal would be CHG + ANE.
CHG is the "Near Eastern" in Teal.

parastais
11-17-2015, 01:21 PM
Teal would be CHG + ANE.
CHG is the "Near Eastern" in Teal.
I might be misreading the text, but my feel was CHG was ~100% teal.

Padre Organtino
11-17-2015, 01:21 PM
Teal would be CHG + ANE.
CHG is the "Near Eastern" in Teal.

If Teal is CHG + ANE then North Caucasians should provide at least a comparable fit to Georgians and Armenians when modeling Yamnaya.

They don't however

parasar
11-17-2015, 01:59 PM
If Teal is CHG + ANE then North Caucasians should provide at least a comparable fit to Georgians and Armenians when modeling Yamnaya.

They don't however

I don’t know what the Teal population is, though I have speculated it is from further east.
Teal is needed so that after admixture ANE does not drop from EHG to Yamnaya.
A simple EHG and CHF* admixture would not work as it would reduce ANE levels.

EDIT: CHG

Padre Organtino
11-17-2015, 02:03 PM
I don’t know what the Teal population is, though I have speculated it is from further east.
Teal is needed so that after admixture ANE does not drop from EHG to Yamnaya.
A simple EHG and CHF admixture would not work as it would reduce ANE levels.

Again, if you assume that there is anything above say 5% additional ANE then North Caucasians who are almost like CHG plus some WHG and ANE (and a little ENF) should be at least
as good as Georgians for the purpose of modeling Teal like admixture (ANE and WHG are of course closer to each other than any of them to CHG).

We don't observe this in formal tests so my guess is there is not much additional ANE ancestry in Yamnaya above what we get from EHG/CHG mix.

parasar
11-17-2015, 02:03 PM
Again, if you assume that there is anything above say 5% additional ANE then North Caucasians who are almost like CHG plus some WHG and ANE (and a little ENF) should be at least
as good as Georgians for the purpose of modeling Teal like admixture (ANE and WHG are of course closer to each other than any of them to CHG).

We don't observe this in formal tests so my guess is there is not much additional ANE ancestry in Yamnaya above what we get from EHG/CHG mix.

I'm going by the following:
1. EHG was WHG related + ANE related.
2. EHG merged with something that had "Near Eastern" ancestry that was different from EEF, to form Yamna.
3. After this merger the ANE related in EHG barely changed, but WHG related dropped, and the "Near Eastern" increased. Ie there was dilution of EHG without a dilution of ANE (please see Haak's PCA below).

So the theory was that the population merging into the EHG was also very ANE rich. I doubt that CHG is that ANE rich merging population.


http://2.bp.blogspot.com/-CuyvqGGHnqQ/VNxUuaBsnYI/AAAAAAAAJ7Y/ZJLiJXASI_U/s1600/2.jpg

Shaikorth
11-17-2015, 02:11 PM
If Teal is CHG + ANE then North Caucasians should provide at least a comparable fit to Georgians and Armenians when modeling Yamnaya.

They don't however

Lazaridis posted at Eurogenes that anything from Lezgins to BedouinB provided a successful fit for Yamnaya, the amount of non-EHG ancestry needed in the fit appeared to increase with ANE (39% BedouinB, 47% Druze, 48% Iraqi Jew, 53% Armenian, 68% Lezgin). Armenians and Iraqi Jews produced the most negative f4(EHG, Yamnaya; X, Chimp) mixture signal so they used those two as the sources in the paper.

The allele frequencies (TreeMix) suggest that Georgians are the best fit among modern populations though.

Padre Organtino
11-17-2015, 02:12 PM
Yamnaya is AFAIK less related to ANE than EHG. At least that's what it looks like from almost all the PCA plots involving the two that I have seen so far.

http://eurogenes.blogspot.ru/2015/06/first-look-at-ancient-genome-from.html

Kurd
11-17-2015, 02:16 PM
Double post

Heber
11-17-2015, 02:17 PM
CHG origins of migrating Early Bronze Age herders
We investigated the temporal stratigraphy of CHG influence by comparing these data to previously published ancient genomes. We find that CHG, or a population close to them, contributed to the genetic makeup of individuals from the Yamnaya culture, which have been implicated as vectors for the profound influx of Pontic steppe ancestry that spread westwards into Europe and east into central Asia with metallurgy, horseriding and probably Indo-European languages in the third millenium BC5, 7. CHG ancestry in these groups is supported by ADMIXTURE analysis (Fig. 1b) and admixture f3-statistics14, 25 (Fig. 5), which best describe the Yamnaya as a mix of CHG and Eastern European hunter-gatherers. The Yamnaya were semi-nomadic pastoralists, mainly dependent on stock-keeping but with some evidence for agriculture, including incorporation of a plow into one burial26. As such it is interesting that they lack an ancestral coefficient of the EF genome (Fig. 1b), which permeates through western European Neolithic and subsequent agricultural populations. During the Early Bronze Age, the Caucasus was in communication with the steppe, particularly via the Maikop culture27, which emerged in the first-half of the fourth millennium BC. The Maikop culture predated and, possibly with earlier southern influences, contributed to the formation of the adjacent Yamnaya culture that emerged further to the north and may be a candidate for the transmission of CHG ancestry. In the ADMIXTURE analysis of later ancient genomes (Fig. 1b) the Caucasus component gives a marker for the extension of Yamnaya admixture, with substantial contribution to both western and eastern Bronze Age samples.

http://www.nature.com/ncomms/2015/151116/ncomms9912/full/ncomms9912.html

This was proposed by Cunliffe in his latest book, "Steppes, Desert and Ocean".

6637

https://www.pinterest.com/gerardcorcoran/steppes-desert-and-ocean/

https://www.pinterest.com/gerardcorcoran/ancient-dna/

Here is a link to "By Steppes, Desert and Ocean".
It describes the movement from Balkans, Uruk, Maikop, Yamnaya.
Cunliffe make the point that this was a passage for wheeled wagons and copper metallurgy from the Balkans via Uruk and Maikop to the Steppes. It could explain the transmission of CHG.
https://books.google.ie/books?id=osQ9CgAAQBAJ&pg=PA95&lpg=PA95&dq=Uruk+Maikop+Yamnaya+cunliffe&source=bl&ots=AruGvBr8cl&sig=8cYDqI7JaBsEVnABpqsXCQCptu8&hl=en&sa=X&ved=0CCMQ6AEwAWoVChMIpcbvrtCXyQIVwgwPCh144w5G#v=on epage&q=Uruk%20Maikop%20Yamnaya%20cunliffe&f=false

Kurd
11-17-2015, 02:17 PM
http://www.anthrogenica.com/attachment.php?attachmentid=6646&stc=1

With this Fig 2, probably CHG has no ANE!
BA Armenian are a mixture and they are different from CHG

What have you seen that leads you to believe that MA1 and BA Armenians form a clade to the exclusion of EF??

Have you forgotton the Dstats I ran?

D(Gorilla, BA Armenian; LBK_EN, MA1) = -0.0448
D(Mbuti, BA Armenian; Stuttgart, MA1)= -0.0273

Shaikorth
11-17-2015, 02:22 PM
Yamnaya is AFAIK less related to ANE than EHG. At least that's what it looks like from almost all the PCA plots involving the twit that I have seen so far.

http://eurogenes.blogspot.ru/2015/06/first-look-at-ancient-genome-from.html

EHG is a better fit than ANE for Native Americans too, and more related to about everyone, but that probably has to do with the fact that MA-1 is too old and 1x coverage.

Padre Organtino
11-17-2015, 02:33 PM
On a sidenote I wonder if we can assume that North Caucasians are a three way mix of EHG, CHG and some ENF? (not accounting for additional recent East Asian like ancestry).

J Man
11-17-2015, 02:35 PM
On a sidenote I wonder if we can assume that North Caucasians are a three way mix of EHG, CHG and some ENF? (not accounting for additional recent East Asian like ancestry).

Modern day North Caucasians obviously have a large amount of Neolithic or ENF ancestry as well.

royking
11-17-2015, 02:42 PM
Ted Kandell from OGF found this sample to be J2a-Y12378. "The sample KK1 from Kotias Klde, Georgia, 9955-9589 ybp (cal BP+60) is
Y12630+ Y12628+ and therefore J-Y12378. However, he's also SK1314/Y12595-, Y12624-, CTS3089-, and therefore a "partial" J-Y12378.
http://www.open-genomes.org/…/Jones%20(2015)%20…/KK1/images/

This is a preliminary result from just 1 out of 5 sequences for KK1, but it seems to be consistent." CEPH also has an Adyghe who is likely from this cluster and ChrisR has several Georgians, a Chechen and an Adyghe from this group.

Chad Rohlfsen
11-17-2015, 03:54 PM
Chad can you specify & detail what exactly you're seeing between all the different basal groups (BE, ANE, whg, CHG, EHG) (sorry if you're repeating yourself).

I think EEF/ Anatolians share a Near Eastern ancestor. EEF/ Anatolia has WHG backflow from the LGM and CHG has crown West Eurasian, to a good degree. This is way before pottery or that pressure flaking people talk about. If pots and flaking always means new genes, where is the ena from pottery and ane with flaking. Where's the ANE in NW africa and Chalcolithic Iberia? Things aren't that simplistic.

paulgill
11-17-2015, 06:00 PM
Ted Kandell from OGF found this sample to be J2a-Y12378. "The sample KK1 from Kotias Klde, Georgia, 9955-9589 ybp (cal BP+60) is
Y12630+ Y12628+ and therefore J-Y12378. However, he's also SK1314/Y12595-, Y12624-, CTS3089-, and therefore a "partial" J-Y12378.
http://www.open-genomes.org/…/Jones%20(2015)%20…/KK1/images/

This is a preliminary result from just 1 out of 5 sequences for KK1, but it seems to be consistent." CEPH also has an Adyghe who is likely from this cluster and ChrisR has several Georgians, a Chechen and an Adyghe from this group.

http://www.open-genomes.org/genomes/Jones%20%282015%29%20Georgia/KK1/images/

vettor
11-17-2015, 06:22 PM
ANE and WHG share more drift with each other than either does with CHG. From the steppe, Europeans received actual ANE input, CHG in steppe groups, and shared ANE/WHG ancestry. From Europe, they received actual WHG input.

" It is interesting to note that Bichon, as well as other WHG, form a clade with both MA1 and EHG to the exclusion of CHG (Supplementary Table 6). This suggests the Ancient North Eurasian (ANE) ancestry and WHG ancestry may have shallower roots and diverged subsequent to splitting from CHG (Supplementary Fig. 2). This is consistent with ADMIXTURE analysis and the geographic range of these groups -CHG were separated from these North Eurasian hunter-gatherers by the Caucasus mountain range"

Since Bichon as per supplementary paper #8 is I2a in switzerland, where do you think this split occurred , the caucasus or central europe ( or along the way )

Anabasis
11-17-2015, 06:43 PM
Lollllllll, So Called "Ancestral North Euroasian" actualy was Ancestral caucasian. Baloon of ANE exploded.

ANE7 and K36 calculator results (on Upper Palaeolithic genome from Satsurblia cave, Georgia):

parasar
11-17-2015, 06:56 PM
I might be misreading the text, but my feel was CHG was ~100% teal.

CHG is as distant to ANE as it is to WHG (see A. below where dsat is 0). A slight change perhaps may be perceptible from Satsurblia to Kotias in terms of increased MA1 affinity.

If Teal is supposed to be nearly 50% ANE, then CHG is not Teal.
http://www.anthrogenica.com/attachment.php?attachmentid=6646&d=1447759008

Kurd
11-17-2015, 07:04 PM
I was about to post something cautioning against reading too much into calculator results for CHG using calculators that source on majority transition SNPs, due to transition substitutions resulting from cytosine deamination because of the age of the genomes, when I received an email from the authors that most of the D and f-statistics were done using just transversions (not shown in the paper). They also performed base recalibration using mapDamage in order to limit the effect misincorporations had on Admixture analyses.

parastais
11-17-2015, 07:19 PM
CHG is as distant to ANE as it is to WHG (see A. below where dsat is 0). A slight change perhaps may be perceptible from Satsurblia to Kotias in terms of increased MA1 affinity.

If Teal is supposed to be nearly 50% ANE, then CHG is not Teal.
http://www.anthrogenica.com/attachment.php?attachmentid=6646&d=1447759008
If...
Let's revisit that. Where does it come from? Could it just be that teal was different from EEF. And this difference (no whg) for the lack of better options was (then) explained by having 50% ANE and 50% ENF?

J Man
11-17-2015, 07:22 PM
Ted Kandell from OGF found this sample to be J2a-Y12378. "The sample KK1 from Kotias Klde, Georgia, 9955-9589 ybp (cal BP+60) is
Y12630+ Y12628+ and therefore J-Y12378. However, he's also SK1314/Y12595-, Y12624-, CTS3089-, and therefore a "partial" J-Y12378.
http://www.open-genomes.org/…/Jones%20(2015)%20…/KK1/images/

This is a preliminary result from just 1 out of 5 sequences for KK1, but it seems to be consistent." CEPH also has an Adyghe who is likely from this cluster and ChrisR has several Georgians, a Chechen and an Adyghe from this group.

It is confirmed 100% now that the Kotias Klde sample that dates back 9,529–9,895 cal. BP from Mesolithic Georgia belongs to Y-DNA haplogroup J2a! :D

Anabasis
11-17-2015, 07:36 PM
It is confirmed 100% now that the Kotias Klde sample that dates back 9,529–9,895 cal. BP from Mesolithic Georgia belongs to Y-DNA haplogroup J2a! :D

He might be grandfather of all J-Y12378 as far as TMRCA of J-Y12378 is just 9200 years in yfull J-Y12378 http://www.yfull.com/tree/J-Y12378/

Arbogan
11-17-2015, 07:42 PM
It would be interesting to see the full extent of their presence in the middle-east. It must have had a substantial impact on anatolia, Iran and northern mesopotamia. Considering how high the amounts of Caucasus-Gedrosia distribution is in non-semitic speaking areas. Now i'm just waiting for samples from the ancient levant, Iran and anatolia to confirm. We also need a decent PCA analysis including modern samples aswell.

Im hoping that they'll continue getting older and more recent samples from the entire region in the future.

Chad Rohlfsen
11-17-2015, 09:20 PM
I think this CHG is going to shake up the Anatolian/EEF tree. You can see on PCA, and drift stats, a shift from Bedouin to Caucasus, going from Spain EN to Hungary EN. With a Natufian, we will see this more clearly.

parasar
11-17-2015, 09:25 PM
Since Bichon as per supplementary paper #8 is I2a in switzerland, where do you think this split occurred , the caucasus or central europe ( or along the way )

Interesting question.
The paper seems to identify an LGM phase - LGM may have caused the formation of these components by isolating populations - CHG, EEF and WHG did not mix with ANE still stuck further east.

http://www.nature.com/ncomms/2015/151116/ncomms9912/images/ncomms9912-f2.jpg




Satsurblia was occupied after this LGM period. "Last Glacial Maximum (LGM) at 24,000–18,000 calibrated years before present (ka cal. BP), a climate event which had a major demographic impact on human populations in Eurasia ...
new evidence in the southern Caucasus for human occupation immediately after the LGM."
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111271

But from where?

J Man
11-17-2015, 09:30 PM
He might be grandfather of all J-Y12378 as far as TMRCA of J-Y12378 is just 9200 years in yfull J-Y12378 http://www.yfull.com/tree/J-Y12378/

Yes and for a final confirmation I emailed the main author of the study and she replied.

''I'm very sorry about the mix up in the supplementary material. The main text is correct - Kotias was assigned to haplogroup J2a and Satsurblia to J.''

parasar
11-17-2015, 09:40 PM
He might be grandfather of all J-Y12378 as far as TMRCA of J-Y12378 is just 9200 years in yfull J-Y12378 http://www.yfull.com/tree/J-Y12378/

Very likely.
Y12378 looks to be a Caucasus specific subclade of J2a.

Arbogan
11-17-2015, 09:48 PM
http://www.nature.com/ncomms/2015/151116/ncomms9912/images/ncomms9912-f1.jpg

I wonder who the west-asians closest to south-caucasians are. Iranians, Kurds, Azeris and Anatolian Turks? It looks like Satsurblia, is probably ancestral to whatever hypothetical ancestry that is "West-asian" or "Caucasus-Gedrosia".

vettor
11-17-2015, 09:53 PM
Interesting question.
The paper seems to identify an LGM phase - LGM may have caused the formation of these components by isolating populations - CHG, EEF and WHG did not mix with ANE still stuck further east.

http://www.nature.com/ncomms/2015/151116/ncomms9912/images/ncomms9912-f2.jpg




Satsurblia was occupied after this LGM period. "Last Glacial Maximum (LGM) at 24,000–18,000 calibrated years before present (ka cal. BP), a climate event which had a major demographic impact on human populations in Eurasia ...
new evidence in the southern Caucasus for human occupation immediately after the LGM."
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111271

But from where?

I have not read this new 2015 karafet paper, but some said that IJ split at 22000 which fits with your presentation

http://www.nature.com/ejhg/journal/v23/n3/full/ejhg2014106a.html

jesus
11-17-2015, 09:57 PM
http://www.nature.com/ncomms/2015/151116/ncomms9912/images/ncomms9912-f1.jpg

I wonder who the west-asians closest to south-caucasians are. Iranians, Kurds, Azeris and Anatolian Turks? It looks like Satsurblia, is probably ancestral to whatever hypothetical ancestry that is "West-asian" or "Caucasus-Gedrosia".
Iranians are listed under south Asia in the supplementary data,
The central/south Asians plotting to the west of CHG are most likely Iranians.

Padre Organtino
11-17-2015, 10:06 PM
Iranians are listed under south Asia in the supplementary data,
The central/south Asians plotting to the west of CHG are most likely Iranians.

Seems legit. Question is what's the reason for this? Do they really have the most similar ancestry to CHG (since the latter probably spent some time in Caspian refugee during LGM) or they are pulled East from South Caucasians due to some additional ASI?

MfA
11-17-2015, 10:14 PM
Seems legit. Question is what's the reason for this? Do they really have the most similar ancestry to CHG (since the latter probably spent some time in Caspian refugee during LGM) or they are pulled East from South Caucasians due to some additional ASI?

Projected PCA is not useful, often misleading..

Arbogan
11-17-2015, 10:17 PM
Seems legit. Question is what's the reason for this? Do they really have the most similar ancestry to CHG (since the latter probably spent some time in Caspian refugee during LGM) or they are pulled East from South Caucasians due to some additional ASI?

ASI in west-iranians is quite low. It amounts to 4-8% or less depending on the individual, in kurds it's lower. West-iranians are relatively rich in gedrosia or west-asian however. Or "ANI" which dienekes hypotheized years ago to be related to a georgian like population, because the west-eurasian signal in south-asians had a high relatibility via D-statistics. This study presenting CHG confirms this. My guess is that gedrosia/ANI is CHG with a minor contribution of something south-central-asian/south asian. Possibly ASI or possibly ASI with something else. The Elamitic language is hypothesized to be related to dravidian languages. This would support this. It would mean eastern bound CHG carriers, went via the Iranian plateau to south-asia, and spread. Since the hypothesized time is 4900-1900 BC, it coincides nicely with elamite civilization.

Padre Organtino
11-17-2015, 10:21 PM
One more quick suggestion. At least from the PCA plot it actually looks like CHG are a little too Eastern (despite apparently not having direct ANE ancestry) to create a perfect Yamnaya "child" with an EHG "spouse". Either it was the more ENF shifted version of CHG or the more SHG-like EHG "parent" involved in the process.
This is again just eyeballing the chart.

parasar
11-17-2015, 10:33 PM
Iranians are listed under south Asia in the supplementary data,
The central/south Asians plotting to the west of CHG are most likely Iranians.

Not Makranis?

Generalissimo
11-17-2015, 10:48 PM
One more quick suggestion. At least from the PCA plot it actually looks like CHG are a little too Eastern (despite apparently not having direct ANE ancestry) to create a perfect Yamnaya "child" with an EHG "spouse". Either it was the more ENF shifted version of CHG or the more SHG-like EHG "parent" involved in the process.
This is again just eyeballing the chart.

Projection bias.

Arbogan
11-17-2015, 10:50 PM
Not Makranis?

No. Why would makranis, plot sligtly east of west-asians? They're basically baloochies modified by SSA.

Gravetto-Danubian
11-17-2015, 11:07 PM
I think EEF/ Anatolians share a Near Eastern ancestor. EEF/ Anatolia has WHG backflow from the LGM and CHG has crown West Eurasian, to a good degree. This is way before pottery or that pressure flaking people talk about. If pots and flaking always means new genes, where is the ena from pottery and ane with flaking. Where's the ANE in NW africa and Chalcolithic Iberia? Things aren't that simplistic.

I agree. Pressure blades, and certainly pottery, came from way way to the east to explain things. Pottery came from Korea ! :)
But I'd modify that Anatolian / EEF farmers are just Natufians admixed with some Anatolian HGs. I am very convinced that - based on archaeology- that before 8000 BC - Anatolia was basically part of Epigravettian Europe. it would look like a Balkan variety of WHG. To its east we might expect to have found some CHG chaps.

alan
11-17-2015, 11:19 PM
:) Yes, I agree that 1) it is quite complicated and 2) my post wasn't clear enough.

I forgot to mention one important thing, namely that we know for sure that the Caucasian/Southern component (now known to correspond to CHG) was "not alone" when it was somehow introduced to the EHG (R1-rich) steppe population. In other words, that source population was rich in both CHG and ANE, with the ANE levels equal to those present in EHG.

Let's assume for a moment that EHG could be considered a mixture of ANE and WHG (though I am not sure if this is a good approximation). In such case, Yamna (and probably the closely related cultures like Sredny Stog and Late Khvalynsk) arose as a consequence of an important merging process that started no later than Early Khvalynsk and was completed by the Yamna period). The two merging populations were the Eastern European population rich in WHG and ANE (or the EHG population, as represented by the Karelian R1a and Early Samara R1b samples) and an unknown "Southern" population that was rich in ANE and CHG. This means that both these ancestral populations included significant levels of ANE, yet these two ANE components (let's call them ANE1 and ANE2) have been separated from each other long time ago. We know that ANE1 in EHG was likely associated with haplogroup R1, so the major questions are:
1) When and how did the ANE2+CHG population arise? Where was it located?
2) What were the Y-DNA haplogroups associated with ANE2 and ANE2+CHG?
3) If ANE2 and ANE2+CHG were associated with haplogroup R1 (R1b) then which subclades of R1 (R1b) were associated with ANE1 and ANE2, respectively?
4) What is the likelihood that EHG (or ANE1+WHG) was associated mostly with R1a, so that the EHG sample from Samara (R1b M269-) was only an "outlier" who did not contribute to the further development of any major steppe or forest-steppe culture?



When I mentioned Khvalynsk I meant the entire territory covered by this large culture, and I agree that some earliest mixing points could have been located further south than Khvalynsk itself. The exact location of that first encounter would of course depend on where the mysterious population rich in both ANE and CHG was located.

AFAIK if my theory that ANE is related to pressure flaked microblades arriving in the Mesolithic then the only south Caucasus culture with them was the Chok???(something like that) culture. That could have mixed with the epi-gravettian CHG hunters who were certainly present in Georgia and Armenia although I think it was from slightly further east in the south Caucasus

alan
11-17-2015, 11:44 PM
The timing of the split suggested is interesting. There is some theory that the Aurignacian of the Caucasus is actually some very early proto-Gravettian type culture derived from the Levantine Ahmarian - much earlier than Europe. Think the date given was about 40000 years ago.

https://instaar.colorado.edu/uploads/people/155/hoffecker-2012-eshe-2.pdf

alan
11-17-2015, 11:46 PM
The timing of the split suggested is interesting. There is some theory that the Aurignacian of the Caucasus is actually some very early proto-Gravettian type culture derived from the Levantine Ahmarian - much earlier than Europe. Think the date given was about 40000 years ago.

https://instaar.colorado.edu/uploads/people/155/hoffecker-2012-eshe-2.pdf

It appears from what I have read that Gravettian traits remained dominant in Georgia and Armenia anyway into the Mesolithic. Climate change through the LGM etc means there was probably a lot of confusing abadonment and modest distance movement back and forth over time.

alan
11-17-2015, 11:53 PM
It just struck me if the unique proto-Gravettian/Ahmarian of c. 38000BC that went into and through the Caucasus is closer to Basal than WHG or certainly some generic west Asian then it helps confined the period in which WHG could have emerged - generally associated with the later European Gravettian. They sound like two pulses from the same Ahmarian source but a with a vey long period between them. Perhaps the WHG signal developed in the Ahmarian in between those waves because they had a very long period in which to do so. So WHG could have developed in Levant/Anatolia prior to the movement of the Gravettians into Europe via Anatolia. This would explain why WHG seems to be present in west and perhaps central Anatolian farmers. It is also interesting that IJ is involved in so much as the Caucasians are J and it appears that the European Gravettians were I.

Krefter
11-18-2015, 12:27 AM
If CHG doesn't have ANE then Caucasians don't have ANE.

Gravetto-Danubian
11-18-2015, 12:36 AM
It just struck me if the unique proto-Gravettian/Ahmarian of c. 38000BC that went into and through the Caucasus is closer to Basal than WHG or certainly some generic west Asian then it helps confined the period in which WHG could have emerged - generally associated with the later European Gravettian. They sound like two pulses from the same Ahmarian source but a with a vey long period between them. Perhaps the WHG signal developed in the Ahmarian in between those waves because they had a very long period in which to do so. So WHG could have developed in Levant/Anatolia prior to the movement of the Gravettians into Europe via Anatolia. This would explain why WHG seems to be present in west and perhaps central Anatolian farmers. It is also interesting that IJ is involved in so much as the Caucasians are J and it appears that the European Gravettians were I.

Anything is possible, and any suggestion tentative without aDNA evidence from a European sample dating 30000 - 15000, but I think 'WHG' developed in Europe during, and because of, the LGM and the obvious separation between the proto-WHG, the "CHG"s (which probably harboured in northern Mesopotamia during the peak LGM, then moved to south Caucasus after 18 kya) and the Levantine forager-proto-Natufians.

I think IJ entered Europe, and I 'developed' in Europe. J developed from IJ somewhere in northern Middle East.

Jean M
11-18-2015, 12:40 AM
AFAIK if my theory that ANE is related to pressure flaked microblades arriving in the Mesolithic then the only south Caucasus culture with them was the Chok???(something like that) culture. That could have mixed with the epi-gravettian CHG hunters who were certainly present in Georgia and Armenia although I think it was from slightly further east in the south Caucasus

Madina Galimova 2006:

Chokh Culture, situated in the eastern part of the northern Caucasus (Fig. 1), demonstrates the development of microlithic techniques during the Final Palaeolithic/Neolithic (Amirkhanov 1986). It is characterised by symmetric and asymmetric trapezes, segments, asymmetric triangles, backed points and original chokh points. Except for these specific points, most of the above-mentioned geometrical tools seem to find analogies in the Vyazivok 4a assemblage. Now the chronology of Chokh Culture is revised from the Final Palaeolithic to the Mesolithic. But the contact of its inhabitants with the population of Middle Dnieper Mesolithic sites seems to be likely. The same contacts appeared to happen between inhabitants of the Final Palaeolithic sites of Satanai in the northwest Caucasus and Surskoi 5 in the Lower Dnieper. Taking into consideration the palaeogeographic situation of both these in the steppe or forest-steppe zone makes this hypothesis probable.

Thus, the question concerning the migration of the population with geometric tools in its lithic inventory from western Asia-the northern Caucasus towards the Dnieper-Donets basin ought to be analysed again on the basis of new data.

6647

Krefter
11-18-2015, 12:59 AM
Perhaps the WHG signal developed in the Ahmarian in between those waves because they had a very long period in which to do so. So WHG could have developed in Levant/Anatolia prior to the movement of the Gravettians into Europe via Anatolia. This would explain why WHG seems to be present in west and perhaps central Anatolian farmers. It is also interesting that IJ is involved in so much as the Caucasians are J and it appears that the European Gravettians were I.

WHG is definitely very old. A Gravettian origin is possible.Bichon is 13,700 years old, but EEF is not significantly more related to WHGs from 8,000 years ago than to him. Bichon shares as much drift with 8,000yo WHGs as 8,000yo WHGs share with each other. He might as well be a WHG from 8,000 years ago. La Brana-1 and Loschbour probably didn't share any significant common ancestry since like 13,000 BC at least. EHG is differnt from WHG, but still very WHG-like. So, a uniform type of WHG was widespread because they had been around for over 14,000 years.

Krefter
11-18-2015, 01:01 AM
The paper didn't use many formal stats to find the relationship between CHG and modern Caucasians. Supp. fig 3 shows that Caucasians share slightly less drift with CHG than Europeans do with WHG. ADMIXTURE makes Caucasians roughly 50% CHG.

parasar
11-18-2015, 01:16 AM
If CHG doesn't have ANE then Caucasians don't have ANE.

Caucasians have some as they are mainly EEF + some South Asian. The South Asian portion should give them some ANE.

And some NE ones such as the Lezgins have a lot more ANE.

J Man
11-18-2015, 01:35 AM
I agree. Pressure blades, and certainly pottery, came from way way to the east to explain things. Pottery came from Korea ! :)
But I'd modify that Anatolian / EEF farmers are just Natufians admixed with some Anatolian HGs. I am very convinced that - based on archaeology- that before 8000 BC - Anatolia was basically part of Epigravettian Europe. it would look like a Balkan variety of WHG. To its east we might expect to have found some CHG chaps.

Like we have been saying the I2c among the Anatolian farmers could have come from Western native Anatolian hunter-gatherers (WHG) while the J2a1 among them could possibly have come from Eastern native Anatolian hunter-gatherers (CHG). Of course this is just speculation at this point.

Krefter
11-18-2015, 03:29 AM
Can someone run these stats?

https://docs.google.com/spreadsheets/d/1TPByWTZL2eOhq21QvpeV-PFe7Ev04FAcxeD-72fyMnA/edit#gid=0

Kurd
11-18-2015, 03:33 AM
I have noticed a couple of posters struggling to find a population related to CHG but with more "ANE" to combine with EHG to form Yamnaya. Who ever said that Yamnaya had to have as much "ANE" as EHG? Folks, there is no need to go beating around the bush to find this CHG related 3rd population, A population with a teal modal component such as CHG combined with an EHG population rich in "ANE", which for all practical purposes could be called WHG1 (the flowchart in the paper shows this WHG1 a/k/a ANE as a sister group to WHG), could do the trick. In fact, that is what the authors are showing with this:

http://i.imgur.com/6H5T8qV.jpg

According to the above Yamnaya is basically modeled as about 50% teal (CHG) + 50% WHG1. This is pretty consistent with what I had from the Eurasia 14- Neolithic calculator:


POP
Karelia_HG
Armenian_BA4
MA1


N_Amerindian
10.01%
0.00%
12.01%


Afansievo_Yamnaya
50.05%
56.34%
43.07%


Kalash
0.00%
0.00%
0.55%


Siberian
0.00%
0.00%
0.16%


S_Amerindian
1.29%
0.00%
7.05%


Sub_Saharan
0.00%
0.00%
0.00%


SE_Asian
0.00%
0.00%
0.00%


E_African
0.00%
0.00%
0.00%


SW_Asian
0.00%
26.41%
0.00%


Neolithic_Balkan_Farmers
0.00%
17.24%
0.00%


SHG_WHG
38.63%
0.00%
12.47%


Early_European_Farmers
0.00%
0.00%
0.00%


S_Indian
0.00%
0.00%
20.78%


Papuan
0.00%
0.00%
3.90%



You will notice that the calculator shows EHG as 50% Yamnaya which is consistent with above plot. It also shows BA Armenian as about 50% Yamnaya, and MA1 as about 43% Yamnaya. Not bad considering the program sampled only about 9K transversion SNPs.

The following figure is also from the paper, and shows sources of admixture into modern populations. Modern populations for which CHG are best approximations include Caucuses, S and Central Asia

http://i.imgur.com/JEcCHKc.jpg

Gravetto-Danubian
11-18-2015, 03:55 AM
I have noticed a couple of posters struggling to find a population related to CHG but with more "ANE" to combine with EHG to form Yamnaya. Who ever said that Yamnaya had to have as much "ANE" as EHG? Folks, there is no need to go beating around the bush to find this CHG related 3rd population, A population with a teal modal component such as CHG combined with an EHG population rich in "ANE", which for all practical purposes could be called WHG1 (the flowchart in the paper shows this WHG1 a/k/a ANE as a sister group to WHG), could do the trick. In fact, that is what the authors are showing with this:

http://i.imgur.com/6H5T8qV.jpg

According to the above Yamnaya is basically modeled as about 50% teal (CHG) + 50% WHG1. This is pretty consistent with what I had from the Eurasia 14- Neolithic calculator:


POP
Karelia_HG
Armenian_BA4
MA1


N_Amerindian
10.01%
0.00%
12.01%


Afansievo_Yamnaya
50.05%
56.34%
43.07%


Kalash
0.00%
0.00%
0.55%


Siberian
0.00%
0.00%
0.16%


S_Amerindian
1.29%
0.00%
7.05%


Sub_Saharan
0.00%
0.00%
0.00%


SE_Asian
0.00%
0.00%
0.00%


E_African
0.00%
0.00%
0.00%


SW_Asian
0.00%
26.41%
0.00%


Neolithic_Balkan_Farmers
0.00%
17.24%
0.00%


SHG_WHG
38.63%
0.00%
12.47%


Early_European_Farmers
0.00%
0.00%
0.00%


S_Indian
0.00%
0.00%
20.78%


Papuan
0.00%
0.00%
3.90%



You will notice that the calculator shows EHG as 50% Yamnaya which is consistent with above plot. It also shows BA Armenian as about 50% Yamnaya, and MA1 as about 43% Yamnaya. Not bad considering the program sampled only about 9K transversion SNPs.

The following figure is also from the paper, and shows sources of admixture into modern populations. Modern populations for which CHG are best approximations include Caucuses, S and Central Asia

http://i.imgur.com/JEcCHKc.jpg

Kurd
Are you saying EHG is WHG plus CHG ?

parasar
11-18-2015, 04:03 AM
I have noticed a couple of posters struggling to find a population related to CHG but with more "ANE" to combine with EHG to form Yamnaya. Who ever said that Yamnaya had to have as much "ANE" as EHG? Folks, there is no need to go beating around the bush to find this CHG related 3rd population, A population with a teal modal component such as CHG combined with an EHG population rich in "ANE", which for all practical purposes could be called WHG1 (the flowchart in the paper shows this WHG1 a/k/a ANE as a sister group to WHG), could do the trick. In fact, that is what the authors are showing with this:
...

I believe I mentioned it. It comes from Haak. Since his Yamna are from the north (Samara), and ANE is very high, and almost unchanged from EHG, it was proposed that the admixing population had to have very high ANE so as to not affect the ANE much. On the other hand ANE clearly drops in Yamna samples from the south. So the admixing population for the southern Yamna samples can be without ANE. What we are in fact seeing is a gradation with no ANE south of the Caucasus to 50%ANE at the Samara Bend. Essentially the admixing population for Haak's Yamna are the southern Yamna and not CHG.

The paper also notes that there has been interaction among the WHG types, and a simple tree is not possible for the WHG types. But it is indeed possible ANE and CHG as they show almost no later interaction after they split. The author for some reason ascribe this lack of interaction to the Caucasus chain for the Mesolithic and before (but not for BA).

Kurd
11-18-2015, 04:09 AM
Kurd
Are you saying EHG is WHG plus CHG ?

Not really. Eurasia 14 calculator is saying that EHG shares 50% of its admixture with Yamnaya, which is basically is what the above plot from the paper is showing. I say shares because ADMIXTURE does not convey direction of gene flow. The calculator also shows the remainder of EHG's admixture as allocated to about 40% WHG and about 10% Amerindian. It is Yamnaya that is about 50% CHG and 50% WHG1 ( I make the distinction WHG vs WHG1, because WHG is the component modal to Loshbour, whereas WHG1 is related to WHG, but is better known as the component shared between EHG and Yamnaya)

Chad Rohlfsen
11-18-2015, 04:12 AM
EHG is not WHG plus CHG. EHG doesn't show any "BE". EHG is also further from EEF than WHG. If EHG was WHG plus CHG, it would be closer to EEF than WHG.

parasar
11-18-2015, 04:23 AM
Are you saying EHG is WHG plus CHG ?

The authors say WHG separated from CHG 46ky back. Not only WHG, but WHG & ANE both separated from CHG & NF - ie there was a north south split.

"These three hunter-gatherer groups [WHG, SHG, Bichon] cannot be related by a simple tree as there are signals of admixture between these groups7. This explains why Bichon does not always form a clade with other WHG to the exclusion of SHG...We also found similar results when we let the Hungarian sample KO12 represent WHG.

Bichon, as well as other WHG, form a clade with both MA1 and EHG to the exclusion of CHG (Supplementary Table 6). This suggests the Ancient North Eurasian (ANE) ancestry and WHG ancestry may have shallower roots and diverged subsequent to splitting from CHG ...

an ancient south (Neolithic farmers and CHG) divergence from the ancient North (WHG and ANE) was the earliest split for these groups"

Arbogan
11-18-2015, 05:02 AM
I have noticed a couple of posters struggling to find a population related to CHG but with more "ANE" to combine with EHG to form Yamnaya. Who ever said that Yamnaya had to have as much "ANE" as EHG? Folks, there is no need to go beating around the bush to find this CHG related 3rd population, A population with a teal modal component such as CHG combined with an EHG population rich in "ANE", which for all practical purposes could be called WHG1 (the flowchart in the paper shows this WHG1 a/k/a ANE as a sister group to WHG), could do the trick. In fact, that is what the authors are showing with this:

http://i.imgur.com/6H5T8qV.jpg

According to the above Yamnaya is basically modeled as about 50% teal (CHG) + 50% WHG1. This is pretty consistent with what I had from the Eurasia 14- Neolithic calculator:


POP
Karelia_HG
Armenian_BA4
MA1


N_Amerindian
10.01%
0.00%
12.01%


Afansievo_Yamnaya
50.05%
56.34%
43.07%


Kalash
0.00%
0.00%
0.55%


Siberian
0.00%
0.00%
0.16%


S_Amerindian
1.29%
0.00%
7.05%


Sub_Saharan
0.00%
0.00%
0.00%


SE_Asian
0.00%
0.00%
0.00%


E_African
0.00%
0.00%
0.00%


SW_Asian
0.00%
26.41%
0.00%


Neolithic_Balkan_Farmers
0.00%
17.24%
0.00%


SHG_WHG
38.63%
0.00%
12.47%


Early_European_Farmers
0.00%
0.00%
0.00%


S_Indian
0.00%
0.00%
20.78%


Papuan
0.00%
0.00%
3.90%



You will notice that the calculator shows EHG as 50% Yamnaya which is consistent with above plot. It also shows BA Armenian as about 50% Yamnaya, and MA1 as about 43% Yamnaya. Not bad considering the program sampled only about 9K transversion SNPs.

The following figure is also from the paper, and shows sources of admixture into modern populations. Modern populations for which CHG are best approximations include Caucuses, S and Central Asia

http://i.imgur.com/JEcCHKc.jpg

Shouldn't CHG be higher in Anatolia and Iran than in Europe? Which page in the supplementary did you find the heatmap?
edit: found it. Anyway, strange.

J Man
11-18-2015, 05:08 AM
The authors say WHG separated from CHG 46ky back. Not only WHG, but WHG & ANE both separated from CHG & NF - ie there was a north south split.

"These three hunter-gatherer groups [WHG, SHG, Bichon] cannot be related by a simple tree as there are signals of admixture between these groups7. This explains why Bichon does not always form a clade with other WHG to the exclusion of SHG...We also found similar results when we let the Hungarian sample KO12 represent WHG.

Bichon, as well as other WHG, form a clade with both MA1 and EHG to the exclusion of CHG (Supplementary Table 6). This suggests the Ancient North Eurasian (ANE) ancestry and WHG ancestry may have shallower roots and diverged subsequent to splitting from CHG ...

an ancient south (Neolithic farmers and CHG) divergence from the ancient North (WHG and ANE) was the earliest split for these groups"

According to the study CHG also diverged/split away from the ancestors of the Neolithic farmers around 25ky back as well.

Krefter
11-18-2015, 05:12 AM
If you think about it.........

>EHG, Siberians, South Asians, and Amerindians clearly have MA1-related ancestry.
>Nothing except assumptions about modeling(Pure Near Eastern is Basal Eurasian+WHG) makes West Asians have MA1-related ancestry.

What Chad, parasar, and others have suggested IMO is totally possible. I dis agree with them that CHG doesn't have ANE in the same sense West Asian's today have ANE. IMO, it's possible there's blood related to WHG in Pure Near Easterns(ENF) but it isn't much more related to WHG than to MA1. So ancestry from unknown ancestors who are closely related to WHG and MA1 added with legitamte MA1-related ancestry cause ANE scores to be high in West Asia. Also, I highly suspect North Caucasians have a lot of Steppe ancestry which includes legitimate MA1 ancestry.

It's possible Basal Eurasian isn't real. It could be WHG/ANE have East Asian or Ust Ishim-related ancestry. All we know is there's a type of West Asian-specific ancestry that's closely related to WHG/MA1 North of the Caucasus and that East Asians are closer to WHG/MA1 than to this West Asian-specific type of ancestry.

Arbogan
11-18-2015, 05:21 AM
Can anyone make sense of the admixture analysis in the supplementary info? It's very low resolution. And it's barely viewable.

Krefter
11-18-2015, 05:32 AM
Can anyone make sense of the admixture analysis in the supplementary info? It's very low resolution. And it's barely viewable.

K=9-15
A Middle Eastern component appears in K=9. From K=9-K=15 CHG is a mixture of Middle Eastern and a South Asian centered component. In Europe the South Asian component first appears in late Neolithic, and today most Europeans and West Asians have membership in it. The rest of West Eurasians score in SHG/EHG/WHG centered component and Middle Eastern component.

K=15-22
In K=15 the older CHG scores 100% in a new Caucasus-centered component but the younger one scores just under 10% in a Middle Eastern component. Caucasus today score almost 50% in Middle Eastern component and over 50% in CHG. From K=15-K=20 nothing really changes.
South Asians are a mixture of CHG component and another South Asian component. Europeans are mostly a mixture of SHG/WHG/EHG+CHG+MIddle Eastern. West Asians are mostly a mixture of CHG+Middle Eastern.
By K=18 it looks like Middle Easterns splits into typical Mediterranean and SW Asian.

Arbogan
11-18-2015, 05:39 AM
K=9-15
A Middle Eastern component appears in K=9. From K=9-K=15 CHG is a mixture of Middle Eastern and a South Asian centered component. In Europe the South Asian component first appears in late Neolithic, and today most Europeans and West Asians have membership in it. The rest of West Eurasians score in SHG/EHG/WHG centered component and Middle Eastern component.

K=15-22
In K=15 the older CHG scores 100% in a new Caucasus-centered component but the younger one scores just under 10% in a Middle Eastern component. Caucasus today score almost 50% in Middle Eastern component and over 50% in CHG. From K=15-K=20 nothing really changes.
South Asians are a mixture of CHG component and another South Asian component. Europeans are mostly a mixture of SHG/WHG/EHG+CHG+MIddle Eastern. West Asians are mostly a mixture of CHG+Middle Eastern.
By K=18 it looks like Middle Easterns splits into typical Mediterranean and SW Asian.

I did read this. But the graphical representation might give us a better idea of the proportions.

Kurd
11-18-2015, 05:44 AM
Shouldn't CHG be higher in Anatolia and Iran than in Europe? Which page in the supplementary did you find the heatmap?
edit: found it. Anyway, strange.

If CHG would have been more modern Caucasian like, then yes, because modern Caucasians are more EF shifted like Iranians and Anatolians. These ancient Caucasians were quite different. The paper has the best fit for Iranians as a mix of LBK and Guarani with an f3 score of -0.011 Z=-7.94, and Turks as LBK and Nganasans.

SC and S Asians on the other hand, they have modeled as a Kotias/Kharia mix.. Abkhasians as Kotias/LBK, Estonians as Kotias/Loshbour. I currently don't have those genomes, so I can't run comparisons for all W Asian populations using Kotias.

Gravetto-Danubian
11-18-2015, 05:50 AM
"These three hunter-gatherer groups [WHG, SHG, Bichon] cannot be related by a simple tree as there are signals of admixture between these groups7. This explains why Bichon does not always form a clade with other WHG to the exclusion of SHG...We also found similar results when we let the Hungarian sample KO12 represent WHG.



This specific sentence certainly makes sense, as Bichon is ancestral to, or related to the ancestor of, other later WHGs, and the 'WHG' component in SHG (IMO).

Arbogan
11-18-2015, 05:57 AM
If CHG would have been more modern Caucasian like, then yes, because modern Caucasians are more EF shifted like Iranians and Anatolians. These ancient Caucasians were quite different. The paper has the best fit for Iranians as a mix of LBK and Guarani with an f3 score of -0.011 Z=-7.94, and Turks as LBK and Nganasans.

SC and S Asians on the other hand, they have modeled as a Kotias/Kharia mix.. Abkhasians as Kotias/LBK, Estonians as Kotias/Loshbour. I currently don't have those genomes, so I can't run comparisons for all W Asian populations using Kotias.

Guaranis are a native American tribe. This is even more perplexing.

Gravetto-Danubian
11-18-2015, 06:00 AM
The closer relationship of CHG to EF/ BE raises some questions for me

1) how will it effect European and Anatolian neolithic genomes samples thus far

2) how does one explain the odd Y haplogroup lineages : ie CHG is mostly J, whg is mostly I; yet whg is closer to R1-dominant EHG and ANE. ( I know autosomal components are more complex and not linear and necessarily tree like).

3) why did it appear as if CHG was a mix of ANE and EF ?

Krefter
11-18-2015, 06:09 AM
This specific sentence certainly makes sense, as Bichon is ancestral to, or related to the ancestor of, other later WHGs, and the 'WHG' component in SHG (IMO).

He probably isn't ancestral to Loschbour, La Brana-1, and K01. He behaves almost exactly like those three much later WHGs in formal stats. So, I think WHG formed during the Ice age, and the WHGs from 8,000 years may not have had much common ancestry since the Ice age. So, the WHG signal shared by La Brana-1, Loschbour, and K01 is probably very old.

Gravetto-Danubian
11-18-2015, 06:17 AM
He probably isn't ancestral to Loschbour, La Brana-1, and K01. He behaves almost exactly like those three much later WHGs in formal stats. So, I think WHG formed during the Ice age, and the WHGs from 8,000 years may not have had much common ancestry since the Ice age. So, the WHG signal shared by La Brana-1, Loschbour, and K01 is probably very old.

I think much of Europe was still being populated by the 14-13 ky mark. So this Bichon guy might have something ancestral

Krefter
11-18-2015, 06:21 AM
I think much of Europe was still being populated by the 14-13 ky mark. So this Bichon guy might have something ancestral

Okay I agree with that. There's a chance he's an ancestor to Loschbour and SHG.

jesus
11-18-2015, 06:39 AM
If CHG would have been more modern Caucasian like, then yes, because modern Caucasians are more EF shifted like Iranians and Anatolians. These ancient Caucasians were quite different. The paper has the best fit for Iranians as a mix of LBK and Guarani with an f3 score of -0.011 Z=-7.94, and Turks as LBK and Nganasans.

SC and S Asians on the other hand, they have modeled as a Kotias/Kharia mix.. Abkhasians as Kotias/LBK, Estonians as Kotias/Loshbour. I currently don't have those genomes, so I can't run comparisons for all W Asian populations using Kotias.

Tajik Pamiris and Makranis are the exceptions in South/south central asia, they are molded as LBK + Native American or Vishwabrahmin respectively. Baloch and Brahuis are both CHG + Kharia, it's kinda weird how they differ from Makranis here, since they are almost identical to them in other runs. It's interesting that North Caucasian models don't have CHG, but LBK + Karitiana/Nganasan and MA1 for Lezgins.

pegasus
11-18-2015, 07:57 AM
K8 Satsurblia
ANE 0.2485
South_Eurasian 0.042
ENF 0.6126
East_Eurasian 0
WHG 0.0692
Oceanian 0
Pygmy 0.0043
Sub-Saharan 0.0234

The results look virtually identical to some Caucasus groups today.

bored
11-18-2015, 08:54 AM
ENF=Farmer. Is dead.

I'm not surprised by the results. It didn't make sense to me Basal Eurasians expanded only with farming. I knew Hunter gatherers of West Asia also had Basal Eurasian. West Asian genetic origins are a lot more complicated than early farmers repopulating the region.

Modern Caucasus look like they might be 50%+ from Upper Paleolithic Caucasus people. The West Asians here are probably happy with the results, they have ancestry from their region from before the Sumerians, way back in very primitive times.

The first farmers of Europe certainly had a lot of Near Eastern hunter gatherer ancestry, which clearly was closely related to hunter gatherers in Europe.

These CHG genomes fit better as Yamnaya's non-EHG ancestors than any moderns. They score almost 100% in "Teal" of the paper's ADMIXTURE. It really looks like they were the Teal people.

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

I've added Hirisplex results of the CHG genomes and new Late Upper Palaeilthic WHG genome to Pre-Historic West Eurasian Phenotype (https://docs.google.com/spreadsheets/d/1xe9sgt0PSt6cUQ3cYp14foBoaVGsOKZBmmHJoKz0HB0/edit#gid=1798287387).

The oldest Caucasus genome(13,300yo) and Swiss genome(13,700yo) had rs12913832 AG, confirming blue eyes are over 13,000 years old. The Swiss genome is our first Brown eyed WHG person.

Both Caucasus genomes and new WHG had CC in rs16891982. The oldest example of derived alleles in that SNP are from Sweden and Anatolia dating to 6000 BC. The new WHG had GG in rs1426654 but both Caucasus guys had AA in rs1426654. Both were Caucasus guys were confirmed to have the C11 haplotype found in 97% of AA rs1426654 today. So, far all pre-Neolithic West Eurasians are mostly derived in rs1426654, except WHG.

With these new data it appears: There was eye-color variation in both West Asia and Europe over 13,000 years ago. Blue eyes probably originated before the LGM. Caucasus had the same pigmentation-related alleles as modern West Asians. Mutations associated with Light skin existed over 13,000 years ago in at least the Caucasus(but certainly elsewhere).

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

This paper tells a lot about origins of South Asians. I'm going to post about it later. Many methods show CHG is the best proxy for non-Eastern ancestors of South Asians. They're basically the Teal, ASI, Wet Asian, signal we've seen for years. They contributed ancestry to all West Eurasians and South Asians, and probably others.

What about ANE in South Asia?

Coldmountains
11-18-2015, 09:35 AM
Tajik Pamiris and Makranis are the exceptions in South/south central asia, they are molded as LBK + Native American or Vishwabrahmin respectively. Baloch and Brahuis are both CHG + Kharia, it's kinda weird how they differ from Makranis here, since they are almost identical to them in other runs. It's interesting that North Caucasian models don't have CHG, but LBK + Karitiana/Nganasan and MA1 for Lezgins.

I have the feeling that this models are very off.After looking at the K8 results ancient Caucasians seem to be very similar to modern Caucasians. Let see what Davidski will say about CHG-admixture in the Caucasus and rest of Asia. I am sure that Persians, Tajiks,Baluch, Caucasians and Pashtuns got much if not even most of their ancestry from CHGs or CHG-related people.

Vadim Verenich
11-18-2015, 09:38 AM
Are those genomes available somewhere?

Vadim Verenich
11-18-2015, 10:03 AM
Ok, i have found links to BAM files myself.
Thank you for your help

Generalissimo
11-18-2015, 10:03 AM
Are those genomes available somewhere?

Alex W. did Satsurblia just now, and he's working on Kotias. I can ask him to get in touch with you if you don't know who I'm talking about.

Btw, the raw data is here..

http://www.ebi.ac.uk/ena/data/view/PRJEB11364

MfA
11-18-2015, 11:03 AM
Satsurblia 13.2 ky
Docecad K12b


32.98% Gedrosia
- Siberian
- Northwest_African
- Southeast_Asian
- Atlantic_Med
7.08% North_European
- South_Asian
0.01% East_African
- Southwest_Asian
- East_Asian
59.02% Caucasus
0.91% Sub_Saharan


Distance ID
17.8 Abhkasians_Y
19.4 Adygei
19.5 Chechens_Y
19.8 Georgians
19.9 North_Ossetians_Y
20.3 Lezgins
20.4 Balkars_Y
20.8 Armenians
21.1 Kumyks_Y
21.4 Armenians_15_Y
21.8 Kurds_Y
22.0 Iranian_D
22.7 Kurd_D
22.9 Armenian_D
24.9 Azerbaijan_Jews
25.1 Turks
25.4 Iranians
25.5 Georgia_Jews
25.8 Uzbekistan_Jews
25.9 Assyrian_D


http://i.imgur.com/VuYBw4j.png


http://i.imgur.com/2uwsWuC.png

Jean M
11-18-2015, 01:58 PM
It comes from Haak. Since his Yamna are from the north (Samara), and ANE is very high, and almost unchanged from EHG, it was proposed that the admixing population had to have very high ANE so as to not affect the ANE much. On the other hand ANE clearly drops in Yamna samples from the south. So the admixing population for the southern Yamna samples can be without ANE. What we are in fact seeing is a gradation with no ANE south of the Caucasus to 50% ANE at the Samara Bend. Essentially the admixing population for Haak's Yamna are the southern Yamna and not CHG.

Makes perfect sense. Razib Khan http://www.unz.com/gnxp/children-of-eden/ has reposted a tweet from Lazarides who seems happy:


In Haak, Lazaridis et al. (2015) we modeled Yamnaya as EHG+Something from the Caucasus/Near East. Quite convinced that CHG is that something

Jean M
11-18-2015, 02:01 PM
Razib Khan draws a sensible conclusion:


Over the past few years we have seen ancient DNA researchers “carve nature at its joints” when it comes to the paleohistory of Europe after the end of the last Ice Age. In relation to this historical reconstruction we aren’t at the end of the road, but I do think that the terminus is within sight.....

Finally, let’s remember that we’re constructing the past from the slim remains which we have on hand. Ten years ago we were using extant genetic variation, because that’s all we had, and that led us astray. In the broadest sketches the inferences were right, but in many details they were misleading. Similarly, we shouldn’t think that the ancient DNA yielding populations are necessarily the direct ancestors of any modern groups. We know, for example, that Ma’lta is actually not ancestral to the ANE population which contributed to both Europeans via the EHG and Native Americans. The ANE drift of these two groups has more in common than with Ma’lta. Like the ancient Ethiopian genome there are many interesting conclusions one can derive from novel results, but to the first carving of nature’s joints is not always the best.

http://www.unz.com/gnxp/children-of-eden/

Vadim Verenich
11-18-2015, 02:37 PM
Alex W. did Satsurblia just now, and he's working on Kotias. I can ask him to get in touch with you if you don't know who I'm talking about.

Btw, the raw data is here..

http://www.ebi.ac.uk/ena/data/view/PRJEB11364

Thanks, ask him of he can get in touch with me.
I'll try to do all 3 genomes myself, but in any case it will be useful to compare the results using the files generated by Alex W.

Mher
11-18-2015, 02:50 PM
Satsurblia 13.2 ky
Docecad K12b


32.98% Gedrosia
- Siberian
- Northwest_African
- Southeast_Asian
- Atlantic_Med
7.08% North_European
- South_Asian
0.01% East_African
- Southwest_Asian
- East_Asian
59.02% Caucasus
0.91% Sub_Saharan


Distance ID
17.8 Abhkasians_Y
19.4 Adygei
19.5 Chechens_Y
19.8 Georgians
19.9 North_Ossetians_Y
20.3 Lezgins
20.4 Balkars_Y
20.8 Armenians
21.1 Kumyks_Y
21.4 Armenians_15_Y
21.8 Kurds_Y
22.0 Iranian_D
22.7 Kurd_D
22.9 Armenian_D
24.9 Azerbaijan_Jews
25.1 Turks
25.4 Iranians
25.5 Georgia_Jews
25.8 Uzbekistan_Jews
25.9 Assyrian_D


http://i.imgur.com/VuYBw4j.png


http://i.imgur.com/2uwsWuC.png

wrong location

J Man
11-18-2015, 02:52 PM
wrong location

Yes the samples are in Georgia not Armenia.

Mher
11-18-2015, 02:54 PM
Satsurblia 13.2 ky
Docecad K12b


32.98% Gedrosia
- Siberian
- Northwest_African
- Southeast_Asian
- Atlantic_Med
7.08% North_European
- South_Asian
0.01% East_African
- Southwest_Asian
- East_Asian
59.02% Caucasus
0.91% Sub_Saharan


Distance ID
17.8 Abhkasians_Y
19.4 Adygei
19.5 Chechens_Y
19.8 Georgians
19.9 North_Ossetians_Y
20.3 Lezgins
20.4 Balkars_Y
20.8 Armenians
21.1 Kumyks_Y
21.4 Armenians_15_Y
21.8 Kurds_Y
22.0 Iranian_D
22.7 Kurd_D
22.9 Armenian_D
24.9 Azerbaijan_Jews
25.1 Turks
25.4 Iranians
25.5 Georgia_Jews
25.8 Uzbekistan_Jews
25.9 Assyrian_D


http://i.imgur.com/VuYBw4j.png


http://i.imgur.com/2uwsWuC.png

Dodecad K12b Oracle results:
The GEDmatch version of Oracle may give slightly different results from Dienekes version. The GEDmatch version uses FST weighting in its calculations.

Kit F322930

Admix Results (sorted):

# Population Percent
1 Caucasus 48.47
2 Gedrosia 18.61
3 Southwest_Asian 14.3
4 Atlantic_Med 10.98
5 North_European 5.14
6 South_Asian 1.75
7 Northwest_African 0.69
8 Southeast_Asian 0.06

Single Population Sharing:

# Population (source) Distance
1 Uzbekistan_Jews (Behar) 6.03
2 Azerbaijan_Jews (Behar) 6.45
3 Georgia_Jews (Behar) 6.88
4 Assyrian (Dodecad) 7.04
5 Armenians_15 (Yunusbayev) 7.1
6 Armenian (Dodecad) 7.28
7 Turks (Behar) 7.84
8 Turkish (Dodecad) 9.11
9 Iranian_Jews (Behar) 10.11
10 Armenians (Behar) 11.35
11 Iraq_Jews (Behar) 11.36
12 Kurds (Yunusbayev) 11.44
13 Kurd (Dodecad) 12.78
14 Druze (HGDP) 13.16
15 Iranian (Dodecad) 13.32
16 Lebanese (Behar) 13.95
17 Cypriots (Behar) 15.25
18 Iranians (Behar) 16.32
19 Syrians (Behar) 17.5
20 Kumyks (Yunusbayev) 18.94
my result with Dodekade 12b

MfA
11-18-2015, 02:57 PM
wrong location

That's predicted location by using modern populations' dodecad k12b results for the specimen, not the cave of Satsurblia.

MfA
11-18-2015, 03:46 PM
Here is an OpenOffice-based spreadsheet that acts as the basic Oracle function from Gedmatch. I modified previous version so you can compare with ancient Armenian samples as well.

You can use it without downloading, just choose "Open with" and then click on google sheets. You can then enter your Dodecad K12b results directly or download the sheet in excel format.
https://drive.google.com/file/d/0B6r2nbGXpVFnWUFzcUJxamZSNWc/view?usp=sharing

Here's my results


Armenia MBA 21.98659583
Armenia LBA 18.72300702
Satsurblia CHG 22.83888847

DMXX
11-18-2015, 04:30 PM
One quick point regarding the Iranian samples; Arbogan determined months back that they are a pan-national cohort. I can only assume north Iranians will have a greater affinity to Satsurblia if they were preferentially sampled. Even then, Jones et al.'s two-way ancestral proportions for Iranians matched other South Caucasians.

Also, CHG will now offer us a much more accurate (but not ideal) set of qpAdm outputs for modern South-Central Asians given the paper's conclusions. At the least, we need Subcontinental ASE to manifest itself through aDNA. Nonetheless, whatever proportions Davidski procures via Andronovo/Sintashta + Satsurblia + 3rdpop combinations will intuitively be much closer to the truth (Jones et al. indicates what many of us have expected for a while, specifically, the South-Central Asian and West Asian connection to the steppes is mostly from common ancestry, exemplified now by CHG).

At least now we can stop using the "teal" descriptor!

Arbogan
11-18-2015, 05:04 PM
I'm looking forward to seeing thsee samples in analysis. Now that we have atleast 2 studies providing us with both almost pure NF and CHGs. We'll get an even better analysis than before for west asians. I predict that south west asian scores will plummet for anatolians/west-iranics while being significantly reduced in levantines/mesopotamians. I honestly wish that there was a more prevalent interest of archaeo-genetics in Iran, turkey, and the levant. Ancient samples from israel-lebanon, eastern turkey and SW/NW iran would give us a more complete picture. But in overall this is a positive development and long over due. I hope this will spark more interest south and east of traditional study areas.

I know that there are many decent samples. Not long ago I remember there was a study on mtdna from neolithic samples in israrl/lebanon.

vettor
11-18-2015, 05:06 PM
Here is an OpenOffice-based spreadsheet that acts as the basic Oracle function from Gedmatch. I modified previous version so you can compare with ancient Armenian samples as well.

You can use it without downloading, just choose "Open with" and then click on google sheets. You can then enter your Dodecad K12b results directly or download the sheet in excel format.
https://drive.google.com/file/d/0B6r2nbGXpVFnWUFzcUJxamZSNWc/view?usp=sharing

Here's my results


Armenia MBA 21.98659583
Armenia LBA 18.72300702
Satsurblia CHG 22.83888847

mine

Armenia MBA 24.008
Armenia LBA 33.185
Satsurblia CHG 59.341

parasar
11-18-2015, 05:16 PM
We are seeing four unadmixed populations within South Asia itself. I can see that the Ongee have been isolated for a long long time, and even the Kusunda, but that the Kharia and Kalash are unadmixed is surprising. The Kharia are a comparatively widespread AA speaking population and for the Kalash the theory goes that they got isolated only in the Islamic period.

Balochi South Asia Kotias Kharia -0.006 0.001 -7.351
Bengali South Asia Kotias Kharia -0.011 0.001 -13.990
Brahui South Asia Kotias Kharia -0.004 0.001 -5.154
Burusho South Asia Satsurblia Korean -0.012 0.001 -11.349
GujaratiA South Asia Kotias Kharia -0.011 0.001 -12.005
GujaratiB South Asia Kotias Kharia -0.012 0.001 -12.427
GujaratiC South Asia Kotias Kharia -0.010 0.001 -10.205
GujaratiD South Asia Kotias Kharia -0.007 0.001 -7.217
Hazara South Asia Spain_EN (I0410) Korean -0.025 0.001 -27.520
Iranian South Asia LBK_EN (I0026) Guarani -0.011 0.001 -7.943
Kalash South Asia Kotias Cabecar 0.016 0.001 11.166
Kharia South Asia Lahu Mala 0.001 0.000 2.675
Kusunda South Asia LBK_EN (I0054) Naxi 0.010 0.001 9.149
Lodhi South Asia Kotias Kharia -0.008 0.001 -10.559
Makrani South Asia LBK_EN (I0046) Vishwabrahmin -0.004 0.001 -5.672
Mala South Asia Kotias Kharia -0.007 0.001 -10.147
Onge South Asia Cambodian Papuan 0.130 0.002 61.297
Pathan South Asia Kotias Kharia -0.011 0.001 -13.879
Punjabi South Asia Kotias Kharia -0.010 0.001 -12.115
Sindhi South Asia Kotias Kharia -0.012 0.001 -15.623
Tiwari South Asia Kotias Kharia -0.012 0.001 -17.322
Vishwabrahmin South Asia Kotias Kharia -0.008 0.001 -12.198



There is also a clear difference between modern North and South Caucasus, with the North showing a distinct ANE type influx lacking in the South.

Abkhasian South Caucasus Kotias LBK_EN (I0046) -0.010 0.002 -5.847
Armenian South Caucasus Satsurblia LBK_EN (I0046) -0.010 0.002 -5.040
Georgian South Caucasus Satsurblia LBK_EN (I0046) -0.011 0.002 -5.469

Adygei North Caucasus LBK_EN (I0026) Karitiana -0.008 0.002 -5.094
Balkar North Caucasus LBK_EN (I0046) Nganasan -0.012 0.001 -9.455
Chechen North Caucasus LBK_EN (I0100) Karitiana -0.007 0.001 -4.741
Kumyk North Caucasus LBK_EN (I0100) Karitiana -0.013 0.001 -8.589
Lezgin North Caucasus LBK_EN (I0046) MA1 -0.010 0.002 -4.737
Nogai North Caucasus LBK_EN (I0046) Nganasan -0.024 0.001 -21.062
North Ossetian North Caucasus LBK_EN (I0046) Nganasan -0.011 0.001 -8.067

Tag Heuer
11-18-2015, 05:44 PM
Here is an OpenOffice-based spreadsheet that acts as the basic Oracle function from Gedmatch. I modified previous version so you can compare with ancient Armenian samples as well.

You can use it without downloading, just choose "Open with" and then click on google sheets. You can then enter your Dodecad K12b results directly or download the sheet in excel format.
https://drive.google.com/file/d/0B6r2nbGXpVFnWUFzcUJxamZSNWc/view?usp=sharing

Here's my results


Armenia MBA 21.98659583
Armenia LBA 18.72300702
Satsurblia CHG 22.83888847

mine:

Participant's results
Armenia MBA 17.150
Armenia LBA 7.977
Satsurblia CHG 23.604

Padre Organtino
11-18-2015, 05:49 PM
Armenian LBA has a clear signal of IE input. No wonder that NCs score close to it - they have some Steppe-like admixture (mostly from maternal side btw)

Tag Heuer
11-18-2015, 05:53 PM
it turns out n. europeans have caucasian admixture as well as some caucasian peoples have n. european admix.

Vadim Verenich
11-18-2015, 06:14 PM
Satsurblia in the latest model of my calculator K16

-----------------------------------------------------------
-- DIY Dodecad v 2.1 --------------------------------------
[email protected]@@@@@@----
-- Copyright (c) 2011 Dienekes Pontikos [email protected]@[email protected]@---
[email protected]@---
-- More information: [email protected]@@@@@@----
----- Dienekes' Anthropology Blog [email protected]@----------
-------- http://dienekes.blogspot.com [email protected]@----------
----- The Dodecad Ancestry Project [email protected]@@@@@@@@---
-------- http://dodecad.blogspot.com ----------------------
-----------------------------------------------------------

16 ancestral populations
116463 total SNPs
2 flipped SNPs
48 heterozygous SNPs
0 no-calls
96979 absent SNPs
0.167298 genotype rate
mode genomewide

96979 SNPs missing (no-call or absent)

3610 dQ: 1.006E-07 goal: 1.000E-07

3614 total iterations
9.999E-08 final dQ

----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

0.00% Amerindian
0.00% Ancestor
30.10% ANE
13.53% ANI
0.00% Arctic
0.00% Australian
56.35% Caucasian
0.00% EastAfrican
0.00% Mesolithic
0.01% NearEast
0.00% Neolithic
0.00% NorthAfrican
0.00% Oceanic
0.00% Siberian
0.00% SouthEastAsian
0.00% Subsaharian

CPU time = 39.02 sec

puntDNALKing
11-18-2015, 06:28 PM
Sorry if someone already answered the question am about the ask, but were can I find the files for these ancient samples?

Edited

Thanks Vadim for answering my question.

Anabasis
11-18-2015, 06:34 PM
Satsurblia in the latest model of my calculator K16

-----------------------------------------------------------
-- DIY Dodecad v 2.1 --------------------------------------
[email protected]@@@@@@----
-- Copyright (c) 2011 Dienekes Pontikos [email protected]@[email protected]@---
[email protected]@---
-- More information: [email protected]@@@@@@----
----- Dienekes' Anthropology Blog [email protected]@----------
-------- http://dienekes.blogspot.com [email protected]@----------
----- The Dodecad Ancestry Project [email protected]@@@@@@@@---
-------- http://dodecad.blogspot.com ----------------------
-----------------------------------------------------------

16 ancestral populations
116463 total SNPs
2 flipped SNPs
48 heterozygous SNPs
0 no-calls
96979 absent SNPs
0.167298 genotype rate
mode genomewide

96979 SNPs missing (no-call or absent)

3610 dQ: 1.006E-07 goal: 1.000E-07

3614 total iterations
9.999E-08 final dQ

----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

0.00% Amerindian
0.00% Ancestor
30.10% ANE
13.53% ANI
0.00% Arctic
0.00% Australian
56.35% Caucasian
0.00% EastAfrican
0.00% Mesolithic
0.01% NearEast
0.00% Neolithic
0.00% NorthAfrican
0.00% Oceanic
0.00% Siberian
0.00% SouthEastAsian
0.00% Subsaharian

CPU time = 39.02 sec

Vadim, I think its time to stop calling Caucaisan component as ANE. Its seems it has not any relationship between Ancestral Nort Euroasian as far as its not in North euroasia.

And i would like to make a complain about your dataset and way of designing your calculators. I investigate the deviations of Mahley and Hodoğlugils Turk_Trabzon samples. Turk_Trabzon averages in your average lists of pops in any MDLP calculator was so great. Most of the real Turk_Trabzon DNA testers results from several comercial companies who uploaded thier files into gedmatch, are not even so close to those averages and they find themselves very close to Armenian Averages. I suspected firstly those samples was not actualy from Trabzon. But when I converted thier ifles into 23AndmE format and then upload them into gedmatch i saw that they matched with Turk_Trabzon samples. While thier Harappa or other caculator results close to our REAL Turk_Trabzon samples thier MDLP calculator have great difference. Of course it might be because of calculator effect but it does not explain the deviation from the averages which is not in dataset. In my opinion you should never use those Mahley and Hodoğlugil samples on forming population averages due to they mostly lack of comercial DNA SNPs.

Padre Organtino
11-18-2015, 06:37 PM
Trabzon Turks will inevitably bear some resemblance with Armenians. Laz and Amshen ancestry are a reason.

Anabasis
11-18-2015, 07:17 PM
Satsurblia 13.2 ky
Docecad K12b


32.98% Gedrosia
- Siberian
- Northwest_African
- Southeast_Asian
- Atlantic_Med
7.08% North_European
- South_Asian
0.01% East_African
- Southwest_Asian
- East_Asian
59.02% Caucasus
0.91% Sub_Saharan


Distance ID
17.8 Abhkasians_Y
19.4 Adygei
19.5 Chechens_Y
19.8 Georgians
19.9 North_Ossetians_Y
20.3 Lezgins
20.4 Balkars_Y
20.8 Armenians
21.1 Kumyks_Y
21.4 Armenians_15_Y
21.8 Kurds_Y
22.0 Iranian_D
22.7 Kurd_D
22.9 Armenian_D
24.9 Azerbaijan_Jews
25.1 Turks
25.4 Iranians
25.5 Georgia_Jews
25.8 Uzbekistan_Jews
25.9 Assyrian_D


http://i.imgur.com/VuYBw4j.png


http://i.imgur.com/2uwsWuC.png

and thats my Dodecad K12b result

Gedrosia 15.35%
Siberian -
Northwest_African 0.48%
Southeast_Asian -
Atlantic_Med 10.13%
North_European 3.15%
South_Asian -
East_African -
Southwest_Asian 11.84%
East_Asian -
Caucasus 59.05%
Sub_Saharan -

Megalophias
11-18-2015, 07:29 PM
We are seeing four unadmixed populations within South Asia itself. I can see that the Ongee have been isolated for a long long time, and even the Kusunda, but that the Kharia and Kalash are unadmixed is surprising. The Kharia are a comparatively widespread AA speaking population and for the Kalash the theory goes that they got isolated only in the Islamic period.

Don't forget that three population f3 statistics are affected by drift, so a negative means admixture but a positive does not necessarily mean no admixture. f3(C; A, B) = f3(C'; A, B) + f2(C, C') where C is the modern population actually tested (e.g. Kalash) and C' is the admixed parent population (e.g. hypothetical admixed Bronze Age ancestors of Kalash). So the drift path between the admixed parent population and the modern population is added to the f3 statistic, which can make it turn out positive even when admixture has occurred. Small isolated/endogamous population and/or a very long time since admixture gives high specific drift and obscures the f3 signal.

Whether or not this is actually the case I don't know, Kharia and Kalash surely have fairly recent paternal admixture but it might not be very much of the autosome. Austro-Asiatics are pulled visibly toward Han on PCA but still pretty close to the South Asian cluster. They have a fair bit of Y hg H even though majority O2a1.

Vadim Verenich
11-18-2015, 08:00 PM
Satsurblia in the latest model of my calculator K16

-----------------------------------------------------------
-- DIY Dodecad v 2.1 --------------------------------------
[email protected]@@@@@@----
-- Copyright (c) 2011 Dienekes Pontikos [email protected]@[email protected]@---
[email protected]@---
-- More information: [email protected]@@@@@@----
----- Dienekes' Anthropology Blog [email protected]@----------
-------- http://dienekes.blogspot.com [email protected]@----------
----- The Dodecad Ancestry Project [email protected]@@@@@@@@---
-------- http://dodecad.blogspot.com ----------------------
-----------------------------------------------------------

16 ancestral populations
116463 total SNPs
2 flipped SNPs
48 heterozygous SNPs
0 no-calls
96979 absent SNPs
0.167298 genotype rate
mode genomewide

96979 SNPs missing (no-call or absent)

3610 dQ: 1.006E-07 goal: 1.000E-07

3614 total iterations
9.999E-08 final dQ

----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

0.00% Amerindian
0.00% Ancestor
30.10% ANE
13.53% ANI
0.00% Arctic
0.00% Australian
56.35% Caucasian
0.00% EastAfrican
0.00% Mesolithic
0.01% NearEast
0.00% Neolithic
0.00% NorthAfrican
0.00% Oceanic
0.00% Siberian
0.00% SouthEastAsian
0.00% Subsaharian

CPU time = 39.02 sec

4 Ancestors Oracle
Version 0.97 by Alexandr Burnashev


16 components mode.
Population data has been read. 500 populations found.
Personal data has been read. 20 approximations mode.
Person: Test1
Threshold of components set to 0.39%


Least-squares method.

Using 1 population approximation:
1 Lezgin @ 11.744658
2 Chechen @ 13.414464
3 Adygei @ 14.322171
4 North_Ossetian @ 15.559762
5 Lak @ 16.542275
6 Balkar @ 17.096389
7 Tabasaran @ 17.212844
8 Avar @ 17.268119
9 Azerbaijani_Dagestan @ 17.915575
10 Georgian_Svan @ 18.497122
11 Abhkasian @ 19.004842
12 Georgian_Imereti @ 19.981193
13 Georgian_Kakheti @ 20.180957
14 Georgian @ 20.193127
15 Kabardin @ 20.295474
16 Georgian_Megrel @ 20.315016
17 Stalskoe @ 20.46631
18 Cirkassian @ 20.591733
19 Adjara @ 21.342976
20 Kurd @ 22.41803
500 iterations.

Using 2 populations approximation:
1 Lezgin+Lezgin @ 11.744658
2 Adygei+Lezgin @ 11.77394
3 Chechen+Lezgin @ 12.402338
4 Lezgin+North_Ossetian @ 12.925233
5 Abhkasian+Lezgin @ 13.086531
6 Adygei+Lak @ 13.262749
7 Adygei+Chechen @ 13.300498
8 Chechen+Chechen @ 13.414464
9 Adygei+Avar @ 13.561225
10 Georgian_Svan+Lezgin @ 13.613669
11 Adygei+Tabasaran @ 13.680159
12 Georgian+Lezgin @ 13.691019
13 Georgian_Megrel+Lezgin @ 13.882545
14 Georgian_Imereti+Lezgin @ 13.919064
15 Balkar+Lezgin @ 13.950577
16 Georgian_WGA+Lezgin @ 13.994457
17 Abhkasian+Lak @ 14.059923
18 Lak+Lezgin @ 14.07651
19 Chechen+North_Ossetian @ 14.246513
20 Abhkasian+Avar @ 14.258689
125250 iterations.

Using 3 populations approximation:
1 50% Lezgin +25% Adygei +25% Lezgin @ 11.404168
2 50% Lezgin +25% Georgian_WGA +25% Lezgin @ 11.52671
3 50% Lezgin +25% Abhkasian +25% Lezgin @ 11.619868
4 50% Adygei +25% Lezgin +25% Lezgin @ 11.77394
5 50% Lezgin +25% Georgian +25% Lezgin @ 11.888611
6 50% Lezgin +25% Adygei +25% Chechen @ 11.929526
7 50% Lezgin +25% Chechen +25% Lezgin @ 12.024823
8 50% Lezgin +25% Georgian_Megrel +25% Lezgin @ 12.028411
9 50% Lezgin +25% Lezgin +25% North_Ossetian @ 12.114427
10 50% Lezgin +25% Georgian_Imereti +25% Lezgin @ 12.129535
11 50% Lezgin +25% Georgian_Svan +25% Lezgin @ 12.163775
12 50% Lezgin +25% Chechen +25% Georgian_WGA @ 12.189996
13 50% Lezgin +25% Abhkasian +25% Chechen @ 12.200902
14 50% Lezgin +25% Georgian_WGA +25% Lak @ 12.212667
15 50% Lezgin +25% Abhkasian +25% Adygei @ 12.258027
16 50% Lezgin +25% Adygei +25% North_Ossetian @ 12.297389
17 50% Lezgin +25% Avar +25% Georgian_WGA @ 12.330079
18 50% Lezgin +25% Adygei +25% Lak @ 12.34972
19 50% Adygei +25% Adygei +25% Afghan_Pashtun @ 12.371999
20 50% Chechen +25% Lezgin +25% Lezgin @ 12.402338
36594066 iterations.

Using 4 populations approximation:
1 Adygei+Lezgin+Lezgin+Lezgin @ 11.404168
2 Georgian_WGA+Lezgin+Lezgin+Lezgin @ 11.52671
3 Abhkasian+Lezgin+Lezgin+Lezgin @ 11.619868
4 Lezgin+Lezgin+Lezgin+Lezgin @ 11.744658
5 Adygei+Adygei+Lezgin+Lezgin @ 11.77394
6 Georgian+Lezgin+Lezgin+Lezgin @ 11.888611
7 Adygei+Chechen+Lezgin+Lezgin @ 11.929526
8 Chechen+Lezgin+Lezgin+Lezgin @ 12.024823
9 Georgian_Megrel+Lezgin+Lezgin+Lezgin @ 12.028411
10 Lezgin+Lezgin+Lezgin+North_Ossetian @ 12.114427
11 Georgian_Imereti+Lezgin+Lezgin+Lezgin @ 12.129535
12 Georgian_Svan+Lezgin+Lezgin+Lezgin @ 12.163775
13 Chechen+Georgian_WGA+Lezgin+Lezgin @ 12.189996
14 Abhkasian+Chechen+Lezgin+Lezgin @ 12.200902
15 Georgian_WGA+Lak+Lezgin+Lezgin @ 12.212667
16 Abhkasian+Adygei+Lezgin+Lezgin @ 12.258027
17 Adygei+Lezgin+Lezgin+North_Ossetian @ 12.297389
18 Avar+Georgian_WGA+Lezgin+Lezgin @ 12.330079
19 Adygei+Lak+Lezgin+Lezgin @ 12.34972
20 Adygei+Adygei+Adygei+Afghan_Pashtun @ 12.371999
21 Chechen+Chechen+Lezgin+Lezgin @ 12.402338
22 Georgian_WGA+Lezgin+Lezgin+Tabasaran @ 12.43758
23 Abhkasian+Lak+Lezgin+Lezgin @ 12.440627
24 Chechen+Georgian+Lezgin+Lezgin @ 12.459996
25 Adygei+Adygei+Lak+Lezgin @ 12.464034
26 Adygei+Georgian_WGA+Lezgin+Lezgin @ 12.480726
27 Adygei+Adygei+Georgian_WGA+Jatt-Haryana @ 12.486077
28 Adygei+Avar+Lezgin+Lezgin @ 12.50581
29 Adygei+Georgian_Svan+Lezgin+Lezgin @ 12.506836
30 Adygei+Adygei+Chechen+Lezgin @ 12.50933
31 Adygei+Georgian+Lezgin+Lezgin @ 12.514216
32 Georgian_Kakheti+Lezgin+Lezgin+Lezgin @ 12.519231
33 Adygei+Chechen+Chechen+Lezgin @ 12.535323
34 Adygei+Lezgin+Lezgin+Tabasaran @ 12.543039
35 Adygei+Georgian_Imereti+Lezgin+Lezgin @ 12.570209
36 Abhkasian+Avar+Lezgin+Lezgin @ 12.571974
37 Chechen+Georgian_Megrel+Lezgin+Lezgin @ 12.57548
38 Adygei+Georgian_Megrel+Lezgin+Lezgin @ 12.581948
39 Chechen+Lezgin+Lezgin+North_Ossetian @ 12.586653
40 Adygei+Afghan_Pashtun+Georgian_WGA+Lezgin @ 12.598558
523104326 iterations.


Gaussian method.
Noise dispersion set to 0.31652

Using 1 population approximation:
1 Lezgin @ 4.613077
2 Chechen @ 5.050199
3 Lak @ 5.091205
4 Avar @ 5.146698
5 Georgian_Imereti @ 5.198968
6 Georgian_Megrel @ 5.25305
7 Tabasaran @ 5.28722
8 Georgian_Kakheti @ 5.321809
9 Georgian @ 5.472173
10 Georgian_Svan @ 5.47362
11 Adjara @ 5.485443
12 Abhkasian @ 5.563018
13 Azerbaijani_Dagestan @ 5.571728
14 Adygei @ 5.583196
15 North_Ossetian @ 5.729529
16 Georgian_Laz @ 5.968126
17 Balkar @ 6.045407
18 Stalskoe @ 6.21119
19 Kabardin @ 6.252619
20 Armenian_EastArmenia @ 6.259266
500 iterations.

Using 2 populations approximation:
1 Lezgin+Lezgin @ 4.613077
2 Georgian+Lezgin @ 4.753965
3 Georgian_Megrel+Lezgin @ 4.761406
4 Abhkasian+Lezgin @ 4.781841
5 Georgian_Imereti+Lezgin @ 4.800049
6 Chechen+Lezgin @ 4.812483
7 Adygei+Lezgin @ 4.853991
8 Avar+Lezgin @ 4.886425
9 Lak+Lezgin @ 4.890358
10 Georgian_Svan+Lezgin @ 4.904211
11 Adjara+Lezgin @ 4.916799
12 Georgian_Kakheti+Lezgin @ 4.919354
13 Georgian+Lak @ 4.941755
14 Georgian_Megrel+Lak @ 4.947741
15 Georgian_WGA+Lezgin @ 4.956583
16 Avar+Georgian @ 4.972524
17 Abhkasian+Lak @ 4.985582
18 Abhkasian+Avar @ 4.987405
19 Avar+Georgian_Megrel @ 4.998152
20 Georgian_Imereti+Lak @ 5.000191
125250 iterations.

pegasus
11-18-2015, 08:39 PM
We are seeing four unadmixed populations within South Asia itself. I can see that the Ongee have been isolated for a long long time, and even the Kusunda, but that the Kharia and Kalash are unadmixed is surprising. The Kharia are a comparatively widespread AA speaking population and for the Kalash the theory goes that they got isolated only in the Islamic period.

Balochi South Asia Kotias Kharia -0.006 0.001 -7.351
Bengali South Asia Kotias Kharia -0.011 0.001 -13.990
Brahui South Asia Kotias Kharia -0.004 0.001 -5.154
Burusho South Asia Satsurblia Korean -0.012 0.001 -11.349
GujaratiA South Asia Kotias Kharia -0.011 0.001 -12.005
GujaratiB South Asia Kotias Kharia -0.012 0.001 -12.427
GujaratiC South Asia Kotias Kharia -0.010 0.001 -10.205
GujaratiD South Asia Kotias Kharia -0.007 0.001 -7.217
Hazara South Asia Spain_EN (I0410) Korean -0.025 0.001 -27.520
Iranian South Asia LBK_EN (I0026) Guarani -0.011 0.001 -7.943
Kalash South Asia Kotias Cabecar 0.016 0.001 11.166
Kharia South Asia Lahu Mala 0.001 0.000 2.675
Kusunda South Asia LBK_EN (I0054) Naxi 0.010 0.001 9.149
Lodhi South Asia Kotias Kharia -0.008 0.001 -10.559
Makrani South Asia LBK_EN (I0046) Vishwabrahmin -0.004 0.001 -5.672
Mala South Asia Kotias Kharia -0.007 0.001 -10.147
Onge South Asia Cambodian Papuan 0.130 0.002 61.297
Pathan South Asia Kotias Kharia -0.011 0.001 -13.879
Punjabi South Asia Kotias Kharia -0.010 0.001 -12.115
Sindhi South Asia Kotias Kharia -0.012 0.001 -15.623
Tiwari South Asia Kotias Kharia -0.012 0.001 -17.322
Vishwabrahmin South Asia Kotias Kharia -0.008 0.001 -12.198



There is also a clear difference between modern North and South Caucasus, with the North showing a distinct ANE type influx lacking in the South.

Abkhasian South Caucasus Kotias LBK_EN (I0046) -0.010 0.002 -5.847
Armenian South Caucasus Satsurblia LBK_EN (I0046) -0.010 0.002 -5.040
Georgian South Caucasus Satsurblia LBK_EN (I0046) -0.011 0.002 -5.469

Adygei North Caucasus LBK_EN (I0026) Karitiana -0.008 0.002 -5.094
Balkar North Caucasus LBK_EN (I0046) Nganasan -0.012 0.001 -9.455
Chechen North Caucasus LBK_EN (I0100) Karitiana -0.007 0.001 -4.741
Kumyk North Caucasus LBK_EN (I0100) Karitiana -0.013 0.001 -8.589
Lezgin North Caucasus LBK_EN (I0046) MA1 -0.010 0.002 -4.737
Nogai North Caucasus LBK_EN (I0046) Nganasan -0.024 0.001 -21.062
North Ossetian North Caucasus LBK_EN (I0046) Nganasan -0.011 0.001 -8.067

http://www.cell.com/ajhg/abstract/S0002-9297(15)00137-8?cc=y=

Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia

I believe the Caucasus like people who arrived in NW South Asia mixed with ASI peoples very early on , remained isolated then again mixed with Indo Iranian groups in the Bronze age and then remained isolated till today.

Kalash K8 Avgs
ANE 34.47
South_Eurasian 13.46
ENF 45.77
East_Eurasian 1.62
WHG 1.01
Oceanian 1.39
Pygmy 0.48
Sub-Saharan 1.79

ZephyrousMandaru
11-18-2015, 09:43 PM
Satsurblia in the latest model of my calculator K16

-----------------------------------------------------------
-- DIY Dodecad v 2.1 --------------------------------------
[email protected]@@@@@@----
-- Copyright (c) 2011 Dienekes Pontikos [email protected]@[email protected]@---
[email protected]@---
-- More information: [email protected]@@@@@@----
----- Dienekes' Anthropology Blog [email protected]@----------
-------- http://dienekes.blogspot.com [email protected]@----------
----- The Dodecad Ancestry Project [email protected]@@@@@@@@---
-------- http://dodecad.blogspot.com ----------------------
-----------------------------------------------------------

16 ancestral populations
116463 total SNPs
2 flipped SNPs
48 heterozygous SNPs
0 no-calls
96979 absent SNPs
0.167298 genotype rate
mode genomewide

96979 SNPs missing (no-call or absent)

3610 dQ: 1.006E-07 goal: 1.000E-07

3614 total iterations
9.999E-08 final dQ

----------------------------
FINAL ADMIXTURE PROPORTIONS:
----------------------------

0.00% Amerindian
0.00% Ancestor
30.10% ANE
13.53% ANI
0.00% Arctic
0.00% Australian
56.35% Caucasian
0.00% EastAfrican
0.00% Mesolithic
0.01% NearEast
0.00% Neolithic
0.00% NorthAfrican
0.00% Oceanic
0.00% Siberian
0.00% SouthEastAsian
0.00% Subsaharian

CPU time = 39.02 sec

Are you releasing a new calculator?

parasar
11-18-2015, 09:50 PM
http://www.cell.com/ajhg/abstract/S0002-9297(15)00137-8?cc=y=

Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia
...


Yes I recall that paper, but based on uniparental markers I doubted its conclusions on that deep an isolation.

Plus another paper had mentioned admixture after 1000bc which is close to my estimate for Aryan (the horse iron kind, skeletal record) entry into India.
"the Kalash possess our oldest estimated date of most recent admixture, of 600BCE (990-210BCE)" http://www.sciencemag.org/content/suppl/2014/02/12/343.6172.747.DC1/Hellenthal.SM.pdf

Shaikorth
11-18-2015, 09:53 PM
The drift caused by excessive endogamy in Kalash makes it impossible to detect their admixture using f3-stats, one would have to use qpAdm which does show it quite well.

Vadim Verenich
11-18-2015, 10:04 PM
Are you releasing a new calculator?

Yes, in December

pegasus
11-18-2015, 10:19 PM
Yes I recall that paper, but based on uniparental markers I doubted its conclusions on that deep an isolation.

Plus another paper had mentioned admixture after 1000bc which is close to my estimate for Aryan (the horse iron kind, skeletal record) entry into India.
"the Kalash possess our oldest estimated date of most recent admixture, of 600BCE (990-210BCE)" http://www.sciencemag.org/content/suppl/2014/02/12/343.6172.747.DC1/Hellenthal.SM.pdf

Yeah thats a bit tooo long. A late Bronze age isolation seems more accurate.

tamilgangster
11-19-2015, 11:05 AM
Davidski's ANE component is made up of MA1 or the non-East Asian side of Native Americans, I don't know which. Anyways, it's not madeup of Caucasus people or anyone with CHG-related stuff, so CHG must have MA1 related ancestry. Where did you see that MA1 shares specific alleles with North Europeans that he doesn't with CHG? And if he does it could be just CHG has Basal Eurasian alleles where North Europeans have ANE/WHG alleles. CHG looks robust to me, they both share almost as much drift with each other as La Brana 1 and Loschbour do with each other.

Davids ANE uses the non east eurasian portion of Karitiana, which skews the "ANE" values for many populations. THe Whole concept of ANE seems to be obsolete with the discovery of these newer HG populations.

MfA
11-19-2015, 11:12 AM
Davids ANE uses the non east eurasian portion of Karitiana, which skews the "ANE" values for many populations. THe Whole concept of ANE seems to be obsolete with the discovery of these newer HG populations.

With future ancient South Asian HG samples, ANE will be obsolete for the most of the Eurasia.

tamilgangster
11-19-2015, 11:47 AM
I'm going by the following:
1. EHG was WHG related + ANE related.
2. EHG merged with something that had "Near Eastern" ancestry that was different from EEF, to form Yamna.
3. After this merger the ANE related in EHG barely changed, but WHG related dropped, and the "Near Eastern" increased. Ie there was dilution of EHG without a dilution of ANE (please see Haak's PCA below).

So the theory was that the population merging into the EHG was also very ANE rich. I doubt that CHG is that ANE rich merging population.


http://2.bp.blogspot.com/-CuyvqGGHnqQ/VNxUuaBsnYI/AAAAAAAAJ7Y/ZJLiJXASI_U/s1600/2.jpg

If CHG is not ANE rich, then please explain how caucasus populations score much higher ANE compared to other EUropean or West Asian populations. CHG seems like the most logical explination. Has David done a ANE K7 run on the CHG population yet. Also a harappa DNA run would be useful also

Kurd
11-19-2015, 12:45 PM
Ok folks, I have finally been able to incorporate all 3 genomes into my dataset, Kotias, Bichon, and Satsurbila. My K14 transversions SNP based ADMIXTURE calculator is showing Kotias and Satsurbila very Gedrosian alligned, and Bichon quite similar to Loushbour. Balochis et al scored the highest CHG. Also, I was able to observe substructure within Yamnaya, where some were very EHG shifted. Here are results for a few members. More ADMIXTURE runs at various K to follow:



IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


.Awale
ID001
0.00%
0.00%
0.42%
0.00%
4.52%
43.75%
0.00%
0.00%
1.13%
0.00%
50.17%
0.00%
0.00%
0.00%


.Bol_Nat
ID001
31.99%
2.03%
7.21%
6.46%
4.77%
0.00%
0.00%
0.36%
0.90%
33.66%
3.55%
2.28%
3.69%
3.11%


.Bored
ID001
31.46%
4.25%
2.85%
6.54%
11.01%
0.00%
7.13%
0.80%
0.00%
33.33%
0.00%
0.00%
0.62%
2.01%


.Dluffy
ID001
34.02%
7.65%
0.76%
5.15%
9.35%
0.00%
2.38%
2.17%
2.14%
36.23%
0.00%
0.13%
0.00%
0.00%


.DMXX
ID001
34.02%
4.29%
2.45%
7.12%
2.96%
1.39%
5.84%
1.21%
1.04%
3.02%
17.43%
17.92%
0.00%
1.29%


.Farid
ID001
41.09%
5.85%
1.79%
8.86%
0.00%
3.44%
0.00%
1.63%
0.37%
14.80%
14.67%
4.78%
0.00%
2.72%


.Jesus
ID001
31.98%
5.04%
2.33%
13.55%
0.00%
2.80%
0.52%
2.66%
0.29%
9.72%
16.11%
12.98%
2.02%
0.00%


.Kandhari
ID001
38.71%
4.74%
11.09%
0.00%
7.23%
0.00%
1.85%
0.43%
0.00%
17.12%
4.21%
7.76%
0.39%
6.47%


.Kenji
ID001
20.66%
3.84%
3.49%
11.00%
10.21%
0.00%
0.00%
4.86%
0.00%
31.01%
3.75%
5.62%
5.55%
0.00%


.KURD
ID001
42.86%
2.35%
6.09%
1.46%
5.68%
2.03%
0.92%
1.68%
0.00%
22.99%
1.42%
3.75%
4.95%
3.83%


.Pak_Gujjar
ID001
35.11%
5.94%
0.00%
5.29%
4.99%
0.91%
0.00%
0.61%
1.40%
33.31%
0.00%
9.18%
2.98%
0.29%


.Passa
ID001
13.30%
0.00%
0.66%
6.57%
19.79%
0.00%
1.83%
1.63%
0.00%
0.00%
7.69%
48.52%
0.00%
0.00%


.Rukha
ID001
41.44%
8.34%
4.42%
1.46%
11.70%
1.04%
2.15%
4.74%
0.78%
15.68%
1.27%
4.48%
2.51%
0.00%


.Varun
ID001
25.04%
5.07%
1.02%
10.55%
0.47%
0.00%
2.71%
0.31%
0.25%
45.16%
0.00%
4.20%
0.00%
5.22%


.Zara
ID001
43.20%
7.37%
0.00%
13.30%
0.00%
4.88%
0.86%
2.61%
0.51%
7.94%
13.01%
5.48%
0.00%
0.85%


.Zephyrous
ID001
36.36%
5.73%
3.48%
2.83%
0.00%
0.00%
0.00%
2.86%
0.37%
1.50%
20.17%
25.71%
0.05%
0.93%


Abkhasian
abh119
48.92%
6.28%
1.34%
2.44%
0.79%
0.00%
2.40%
2.45%
0.65%
3.09%
0.47%
29.26%
0.00%
1.92%


Abkhasian
abh41
36.50%
3.16%
6.69%
7.35%
6.97%
0.17%
0.00%
2.83%
0.00%
2.26%
6.51%
26.51%
0.00%
1.04%


Abkhasian
abh147
37.32%
5.10%
5.12%
5.47%
4.01%
0.00%
1.02%
0.00%
0.00%
0.00%
3.80%
34.15%
3.11%
0.90%


Abkhasian
abh27
47.50%
2.39%
4.10%
0.00%
4.00%
1.67%
0.50%
4.07%
0.00%
0.00%
2.27%
30.26%
2.44%
0.80%


Abkhasian
abh24
40.59%
3.26%
4.05%
6.35%
0.26%
1.19%
2.56%
2.91%
0.69%
0.00%
3.57%
33.67%
0.47%
0.43%

Kurd
11-19-2015, 12:48 PM
IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


SATSURBILA
HL
80.50%
0.00%
10.40%
0.00%
0.00%
3.99%
0.00%
2.92%
2.18%
0.00%
0.00%
0.00%
0.00%
0.00%


RISE_baArm
RISE416
76.17%
0.00%
0.00%
0.00%
21.41%
0.00%
2.41%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%


KOTIAS
KK1
63.76%
7.24%
10.15%
5.65%
0.00%
0.00%
0.00%
1.00%
0.94%
0.00%
1.77%
6.37%
2.06%
1.06%


RISE_irArm
RISE408
59.62%
0.00%
21.50%
0.00%
18.88%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%


Makrani
HGDP00158
59.39%
6.47%
3.60%
2.32%
0.00%
4.21%
0.00%
0.00%
0.00%
11.60%
2.63%
2.84%
6.94%
0.00%


Brahui
HGDP00025
57.62%
4.24%
0.00%
4.24%
3.76%
0.00%
2.30%
1.59%
0.73%
16.18%
7.44%
1.82%
0.00%
0.08%


Balochi
HGDP00086
56.18%
4.08%
0.00%
0.00%
6.54%
0.00%
0.00%
0.75%
0.00%
18.33%
9.82%
0.00%
1.47%
2.81%


Brahui
HGDP00045
55.18%
4.85%
0.00%
5.34%
2.76%
0.00%
4.58%
2.27%
0.57%
15.03%
9.42%
0.00%
0.00%
0.00%


Balochi
HGDP00052
53.96%
8.73%
0.00%
5.76%
1.61%
0.00%
0.00%
0.00%
0.00%
17.73%
6.51%
0.00%
4.75%
0.94%


Makrani
HGDP00148
53.67%
0.00%
1.37%
4.10%
7.84%
3.45%
0.00%
4.16%
1.49%
13.52%
4.44%
4.76%
0.00%
1.18%


Brahui
HGDP00033
53.20%
3.42%
0.00%
5.06%
0.93%
0.00%
0.16%
4.44%
0.00%
14.94%
7.45%
10.39%
0.00%
0.00%


Brahui
HGDP00005
53.02%
5.28%
0.00%
2.71%
6.47%
0.00%
1.52%
0.00%
0.00%
19.30%
6.07%
0.00%
4.77%
0.86%


Makrani
HGDP00151
52.13%
5.17%
3.41%
0.65%
0.00%
2.79%
0.39%
1.52%
0.02%
14.57%
13.51%
4.29%
1.56%
0.00%


Makrani
HGDP00131
52.02%
3.90%
2.80%
0.00%
3.72%
4.48%
3.50%
0.23%
0.00%
16.74%
4.84%
6.49%
0.00%
1.27%


Makrani
HGDP00133
52.01%
1.43%
2.00%
7.20%
1.27%
3.88%
0.00%
0.00%
1.04%
16.63%
2.62%
8.94%
0.00%
2.96%


Brahui
HGDP00007
51.98%
0.63%
2.71%
8.91%
0.46%
2.88%
0.00%
2.01%
0.00%
16.30%
3.27%
5.60%
0.00%
5.25%


Brahui
HGDP00011
51.58%
0.63%
0.00%
9.92%
0.25%
1.54%
0.00%
3.24%
0.39%
14.70%
7.44%
7.15%
0.00%
3.15%


Makrani
HGDP00135
51.33%
3.46%
2.44%
5.19%
6.83%
0.00%
0.64%
0.71%
0.88%
17.94%
6.24%
2.65%
0.00%
1.70%


Makrani
HGDP00134
51.05%
3.98%
3.04%
3.62%
1.58%
5.84%
0.00%
1.38%
1.09%
11.77%
10.86%
3.09%
2.71%
0.00%


Brahui
HGDP00023
50.79%
1.37%
6.10%
10.63%
0.72%
2.25%
0.00%
0.77%
0.24%
17.28%
7.50%
0.00%
0.00%
2.35%


Makrani
HGDP00137
50.69%
3.85%
0.00%
11.99%
5.25%
4.52%
1.40%
3.13%
0.00%
9.19%
5.60%
3.73%
0.63%
0.00%


Brahui
HGDP00003
50.56%
2.91%
3.37%
2.58%
0.00%
1.12%
0.42%
1.72%
0.05%
21.44%
1.48%
11.59%
2.72%
0.04%


Balochi
HGDP00080
50.49%
4.13%
2.31%
3.98%
1.62%
2.42%
0.00%
2.73%
0.01%
16.72%
6.62%
5.97%
0.00%
2.98%


Brahui
HGDP00043
49.94%
3.71%
1.52%
5.60%
2.04%
2.56%
3.11%
3.15%
0.49%
18.69%
8.69%
0.00%
0.00%
0.48%


Brahui
HGDP00017
49.94%
7.72%
0.00%
7.22%
1.69%
1.24%
0.68%
0.00%
0.64%
18.43%
3.64%
6.71%
2.10%
0.00%


Brahui
HGDP00001
49.73%
8.95%
3.12%
2.33%
3.07%
2.02%
7.31%
0.32%
0.00%
15.08%
8.08%
0.00%
0.00%
0.00%


Brahui
HGDP00035
49.57%
4.41%
2.75%
6.81%
0.00%
1.08%
9.59%
0.98%
0.00%
13.54%
7.98%
3.30%
0.00%
0.00%


Balochi
HGDP00064
49.35%
5.27%
3.30%
3.92%
0.46%
2.14%
0.00%
2.27%
0.00%
13.63%
13.76%
3.61%
0.00%
2.28%

Kurd
11-19-2015, 12:52 PM
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian


EHG
0.15














Yamanya
0.19
0.22













Kalash
0.08
0.15
0.19












WHG
0.10
0.14
0.19
0.11











W_African
0.17
0.22
0.26
0.17
0.18










SE_Asian
0.14
0.19
0.23
0.13
0.15
0.18









Onge
0.19
0.24
0.29
0.19
0.21
0.23
0.17








Archaic_Human
0.49
0.55
0.60
0.50
0.51
0.42
0.51
0.56







Paniya
0.10
0.16
0.20
0.09
0.12
0.15
0.10
0.15
0.49






E_African
0.11
0.18
0.22
0.12
0.12
0.16
0.16
0.21
0.49
0.12





Balkan NF
0.09
0.15
0.20
0.10
0.11
0.17
0.16
0.21
0.50
0.12
0.11




E_Asian
0.15
0.20
0.24
0.14
0.16
0.19
0.07
0.18
0.52
0.11
0.17
0.17



Siberian
0.16
0.21
0.26
0.15
0.17
0.21
0.10
0.20
0.53
0.14
0.18
0.18
0.09

Kurd
11-19-2015, 01:01 PM
The component values for Kotias, Satsurbila, BA/IA Armenians should not be taken too literally from the above, as they were allowed to form their own component, so that I could get an idea what others scored in terms of CHG. To get a more accurate idea of their values, I will take them out of the ADMIXTURE run, and run them through the calculator itself.

Subsequent ADMIXTURE runs will involve transition and transversion SNPs, with a much higher SNP count for sourcing allele frequencies.

alan
11-19-2015, 01:25 PM
How would you date this hypothetical second wave out of Siberia? Did this smallish (and I guess relatively late) band of people have enough time to nearly double the level of ANE among the local majority (so ANE could reach the previous level after intensive mixing with CHG)?

I would put one as represented by the microblades spreading into eastern/NE Europe and the north fringes of SW Asia about 9500-8000BC. I would see at least one, maybe more waves from Siberia represented by pointed base pots about 6000BC or so.

alan
11-19-2015, 01:47 PM
David just did some analysis over at Eurogenes and concluded my impression is that Satsurblia essentially represents a sister clade of Kostenki, albeit with Mota-related and MA1-related admixtures.

Now given that this person is over 13000 years old that would seem to pre-date the spread of pressure flaked microblades c. 11500 years ago that I have long theorised is connected to ANE spreading west. So, if David is Correct that there is a MA1/ANE admixture then this would imply that ANE made it west at least 1500 years before the microblade model would predict it. Also AFAIK pressure flaked microblades are only known in the south Caucasus east of Georgia. However, its still well post-LGM. I suppose there was real barrier to an early spread of ANE from southern Siberia along Inner Asia/the Stans to reach the Caucasus.

parasar
11-19-2015, 03:44 PM
If CHG is not ANE rich, then please explain how caucasus populations score much higher ANE compared to other EUropean or West Asian populations. CHG seems like the most logical explination. Has David done a ANE K7 run on the CHG population yet. Also a harappa DNA run would be useful also

CHG is not ANE rich. Nor are S. Caucasus populations. N. Caucasus populations such as the Lezgins indeed do have high ANE levels.

All we see is a slight gradation towards ANE from Stuttgart to Sarsurblia to Kotias. This is seen in the Dstats:

D(Yoruba,MA1;Satsurblia,Stuttgart)= D:-0.0096, Z:-1.423
D(Yoruba,MA1;Kotias,Stuttgart) = D:-0.0153, Z:-2.380

This is just not enough affinity to MA1 for the CHG to be deemed "ANE rich." ANE rich was characterized as a population that had about the same level of ANE as EHG.

Please note that I'm not saying that CHG is not the admixing population that formed Yamna-Samara, just that CHG is not that ANE rich population. For that ANE rich population we need to look further north of CHG to the northern Caucasus and the southern Yamna, and we will see a cline of increasing ANE from CHG to Yamna-Samara, reaching 50% ANE levels at the Samara Bend.

parasar
11-19-2015, 04:11 PM
IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


SATSURBILA
HL
80.50%
0.00%
10.40%
0.00%
0.00%
3.99%
0.00%
2.92%
2.18%
0.00%
0.00%
0.00%
0.00%
0.00%


RISE_baArm
RISE416
76.17%
0.00%
0.00%
0.00%
21.41%
0.00%
2.41%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%


KOTIAS
KK1
63.76%
7.24%
10.15%
5.65%
0.00%
0.00%
0.00%
1.00%
0.94%
0.00%
1.77%
6.37%
2.06%
1.06%


Makrani
HGDP00158
59.39%
6.47%
3.60%
2.32%
0.00%
4.21%
0.00%
0.00%
0.00%
11.60%
2.63%
2.84%
6.94%
0.00%




This is fantastic. Are you seeing a cline of slightly reduced CHG levels going north from Makran to the Burusho region?
Also is possible for you to compare the CHG vs the Makrani/Brahui/Baloch on their Denisovan affinity. We may be close here to identifying what has been deemed Basal Eurasian.

Tolan
11-19-2015, 04:22 PM
Ok folks, I have finally been able to incorporate all 3 genomes into my dataset, Kotias, Bichon, and Satsurbila. My K14 transversions SNP based ADMIXTURE calculator is showing Kotias and Satsurbila very Gedrosian alligned, and Bichon quite similar to Loushbour. Balochis et al scored the highest CHG. Also, I was able to observe substructure within Yamnaya, where some were very EHG shifted. Here are results for a few members. More ADMIXTURE runs at various K to follow:


What is Yamnaya in your calculator?
I think we can't put the components of different ages in one calcultrice, especially if one or more components are descendants of others.

parasar
11-19-2015, 04:41 PM
This is fantastic. Are you seeing a cline of slightly reduced CHG levels going north from Makran to the Burusho region?
Also is possible for you to compare the CHG vs the Makrani/Brahui/Baloch on their Denisovan affinity. We may be close here to identifying what has been deemed Basal Eurasian.

To clarify why I was bringing Denisoval in - as I think a lack of Denisovan correlates with increased basal.


It is my thinking that ~40% of Gedrosian is ANE and the rest ~60% basal West Eurasian.

We know the following:
1. Basal West Eurasian and ANE have very little affinity to each other so [they] may [be] thought of as nearly independent and if present complementary - ie one comes at the other's expense when summed as a modern component like Gedrosia.
2. Gedrosia goes down as we go north along the Indus (Brahui to Burusho).
3. ANE goes up as we go north along the Indus (Brahui to Burusho).

But the rise in ANE as we go north is not able to compensate for the decrease in basal West Eurasian, indicating to me that the latter is a slightly larger component of Gedrosia than the former.

That south-west Indus region (Makran/Balochistan) actually may be the point where basal Eurasian originates based on its Denisovan minima.

Kurd
11-19-2015, 05:01 PM
This is fantastic. Are you seeing a cline of slightly reduced CHG levels going north from Makran to the Burusho region?
Also is possible for you to compare the CHG vs the Makrani/Brahui/Baloch on their Denisovan affinity. We may be close here to identifying what has been deemed Basal Eurasian.

Yes, I had to rush out to a meeting early. I will be posting later today

vettor
11-19-2015, 05:18 PM
CHG is not ANE rich. Nor are S. Caucasus populations. N. Caucasus populations such as the Lezgins indeed do have high ANE levels.

.

you can include the much forgotten dagestani with the Lezkgins , they have the high ANE as well

Awale
11-19-2015, 05:46 PM
Yes, I had to rush out to a meeting early. I will be posting later today

Do the Sheikh a favor, broski and include me but don't include something like a mixed "East African" component that would gobble up my West Eurasian side. Just create a standard "SSA" component that would gobble up whatever African ancestry I have; I'd like to see what particular West and/or generally Eurasian components I show up with then. If that won't be too much of an inconvenience, of course. :)

Arbogan
11-19-2015, 07:08 PM
I would like to be included in your runs aswell kurd, if it's possible. I usually score high teal on admixture tests. I wonder if this corresponds to CHG affinity.

Kurd
11-19-2015, 08:09 PM
Do the Sheikh a favor, broski and include me but don't include something like a mixed "East African" component that would gobble up my West Eurasian side. Just create a standard "SSA" component that would gobble up whatever African ancestry I have; I'd like to see what particular West and/or generally Eurasian components I show up with then. If that won't be too much of an inconvenience, of course. :)

Sorry Sheikh, I will start fine tuning your side, once I have this CHG business squared away :)

Kurd
11-19-2015, 08:10 PM
I would like to be included in your runs aswell kurd, if it's possible. I usually score high teal on admixture tests. I wonder if this corresponds to CHG affinity.

I'll PM u a later today with instructions to get included in future projects

Kurd
11-19-2015, 09:26 PM
This is fantastic. Are you seeing a cline of slightly reduced CHG levels going north from Makran to the Burusho region?
Also is possible for you to compare the CHG vs the Makrani/Brahui/Baloch on their Denisovan affinity. We may be close here to identifying what has been deemed Basal Eurasian.

The autosomal structure of CHG seems to have been best preserved by Balochis Brahuis and Makranis . Kalash may be another contender, but I would have to remove all of them except for one from the run to get an idea. I am not sure what the margin of error is of any Denisovan/Neanderthal scores using ADMIXTURE, especially when the sampling is at lower SNP counts such as is the case here.

Here are some additional populations:



IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


Kurd_C1
ID001
45.39%
5.46%
1.06%
0.00%
1.56%
0.00%
0.00%
0.00%
0.65%
1.71%
15.36%
22.36%
0.84%
5.62%


Kurd_C2
ID001
36.80%
0.00%
2.21%
4.95%
6.27%
0.24%
3.58%
3.42%
0.32%
1.98%
6.32%
30.94%
0.95%
2.02%


Burusho
HGDP00438
35.55%
2.16%
0.33%
11.89%
9.41%
0.00%
0.00%
3.32%
0.00%
21.17%
0.00%
3.88%
9.28%
3.00%


Burusho
HGDP00364
30.19%
3.50%
1.97%
12.83%
9.14%
0.00%
6.98%
0.00%
1.06%
20.87%
0.48%
3.81%
6.07%
3.11%


Burusho
HGDP00338
34.20%
5.86%
1.29%
9.40%
8.95%
0.46%
4.43%
4.97%
1.94%
16.12%
0.00%
1.41%
7.72%
3.26%


Burusho
HGDP00423
31.12%
7.70%
0.75%
9.52%
8.81%
1.58%
2.33%
0.91%
0.00%
19.27%
5.82%
0.39%
9.63%
2.18%


Burusho
HGDP00341
32.21%
1.66%
2.46%
11.49%
8.08%
0.00%
0.00%
3.96%
1.11%
20.61%
0.00%
3.84%
14.59%
0.00%


Burusho
HGDP00428
42.04%
4.36%
1.16%
0.00%
7.48%
0.46%
1.77%
1.91%
0.18%
29.09%
0.00%
5.06%
5.05%
1.44%


Burusho
HGDP00346
35.51%
7.65%
1.99%
0.00%
6.91%
0.19%
4.04%
4.77%
0.00%
19.59%
0.00%
5.86%
5.08%
8.39%


Burusho
HGDP00445
30.37%
7.48%
6.13%
1.88%
6.87%
0.00%
4.21%
0.00%
0.00%
24.25%
3.71%
3.76%
6.08%
5.24%


Burusho
HGDP00336
27.97%
5.64%
3.06%
12.80%
6.82%
0.00%
4.11%
1.32%
0.70%
25.30%
1.72%
0.00%
5.82%
4.73%


Burusho
HGDP00359
34.49%
3.22%
4.94%
4.72%
6.65%
0.51%
7.15%
2.57%
0.04%
22.37%
4.69%
1.12%
2.57%
4.97%


Burusho
HGDP00402
29.83%
6.38%
5.12%
4.86%
6.49%
2.32%
5.81%
4.36%
0.00%
26.95%
0.00%
0.15%
3.01%
4.73%


Burusho
HGDP00371
31.26%
8.37%
1.86%
9.48%
5.90%
0.00%
0.00%
0.00%
1.54%
27.13%
0.00%
0.00%
13.06%
1.40%


Burusho
HGDP00433
35.41%
6.65%
3.58%
10.31%
5.59%
0.00%
5.50%
1.26%
0.00%
24.55%
4.86%
0.00%
1.79%
0.51%


Burusho
HGDP00407
29.34%
0.03%
8.18%
10.12%
5.16%
0.00%
6.97%
1.63%
0.09%
23.08%
0.00%
6.00%
6.97%
2.42%


Burusho
HGDP00356
39.13%
7.11%
5.75%
7.73%
4.61%
0.00%
8.99%
0.00%
0.28%
18.44%
0.00%
0.00%
7.96%
0.00%


Burusho
HGDP00388
36.65%
0.00%
7.20%
4.17%
4.19%
2.30%
5.62%
2.26%
0.77%
22.58%
2.14%
2.60%
5.73%
3.79%


Burusho
HGDP00392
35.80%
3.28%
4.69%
13.27%
3.77%
0.00%
5.45%
0.00%
0.23%
20.31%
0.00%
1.58%
0.00%
11.61%


Burusho
HGDP00351
39.81%
2.59%
3.03%
5.04%
3.13%
0.00%
5.35%
5.49%
0.84%
24.50%
1.69%
3.78%
4.49%
0.26%


Burusho
HGDP00444
35.47%
8.31%
4.53%
7.51%
2.97%
0.50%
1.69%
0.00%
0.13%
26.35%
0.80%
0.36%
8.87%
2.51%


Burusho
HGDP00382
30.82%
7.64%
2.06%
7.72%
2.80%
0.28%
2.45%
0.00%
2.07%
24.11%
0.00%
7.69%
11.74%
0.61%


Burusho
HGDP00372
33.72%
4.03%
5.73%
11.57%
2.47%
1.20%
1.55%
3.41%
0.00%
24.31%
0.00%
1.57%
9.37%
1.07%


Burusho
HGDP00412
34.57%
10.38%
4.65%
1.38%
2.27%
0.53%
2.05%
3.89%
0.00%
23.67%
0.99%
6.24%
6.03%
3.34%


Burusho
HGDP00417
28.41%
8.86%
4.98%
10.75%
2.24%
0.00%
5.46%
4.18%
1.25%
20.54%
5.21%
0.00%
8.10%
0.00%

Kurd
11-19-2015, 09:27 PM
IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


Kashmiri_Pandit
PAND_JK4D
26.29%
3.92%
0.72%
8.09%
9.32%
0.00%
6.64%
1.88%
0.66%
34.35%
6.32%
0.00%
0.74%
1.07%


Kashmiri_Pandit
PAND_JK1D
27.87%
4.02%
0.44%
10.49%
8.81%
0.00%
3.10%
4.16%
0.00%
31.01%
0.00%
8.17%
1.91%
0.00%


Kashmiri_Pandit
Kashmiri_Pandit_122_R1
30.05%
2.98%
4.10%
6.80%
8.05%
0.99%
1.24%
3.07%
0.00%
32.79%
0.00%
6.48%
3.45%
0.00%


Kashmiri_Pandit
Kashmiri_Pandit_121_R1
36.34%
7.69%
3.06%
2.56%
7.79%
0.00%
5.11%
4.89%
0.00%
29.29%
0.00%
0.64%
2.62%
0.00%


Kashmiri_Pandit
PAND_JK3D
29.03%
0.00%
5.16%
7.87%
6.93%
0.04%
1.30%
2.42%
0.25%
32.32%
0.00%
11.29%
2.20%
1.19%


Kashmiri_Pandit
Kashmiri_Pandit_125_R1
32.57%
3.17%
2.82%
11.05%
1.29%
0.00%
2.21%
5.26%
1.86%
32.62%
0.00%
5.00%
0.00%
2.14%


Kashmiri_Pandit
PAND_JK1F
37.34%
3.50%
6.18%
5.69%
1.20%
0.00%
1.08%
2.98%
0.00%
30.75%
0.00%
4.53%
3.87%
2.90%


Kashmiri_Pandit
Kashmiri_Pandit_123_R1
37.72%
0.04%
6.41%
6.48%
0.76%
0.00%
7.69%
5.32%
0.59%
29.05%
3.28%
0.00%
0.00%
2.65%


Iranian
iran2
37.69%
7.03%
3.02%
8.81%
5.78%
2.72%
2.81%
1.91%
0.00%
0.48%
11.76%
17.28%
0.00%
0.71%


Iranian
iran20
29.22%
5.09%
1.45%
7.75%
4.10%
2.17%
4.08%
1.22%
0.00%
2.88%
14.02%
27.40%
0.61%
0.00%


Iranian
iran14
31.14%
3.69%
7.45%
9.93%
2.82%
0.24%
0.00%
2.86%
0.03%
9.50%
8.39%
22.87%
0.00%
1.09%


Iranian
iran11
37.11%
4.00%
2.77%
5.52%
2.72%
1.70%
0.21%
7.09%
0.45%
0.99%
6.77%
25.81%
4.41%
0.45%


Iranian
iran19
28.95%
4.12%
6.43%
7.24%
2.23%
2.18%
4.55%
4.13%
1.04%
0.00%
11.76%
27.37%
0.00%
0.00%


Iranian
iran3
35.65%
0.00%
2.89%
0.40%
1.52%
0.00%
0.00%
2.65%
0.42%
9.15%
20.08%
22.05%
0.00%
5.19%


Iranian
iran17
38.32%
3.73%
4.31%
5.78%
0.81%
0.85%
0.00%
1.88%
0.00%
3.97%
8.75%
26.34%
2.94%
2.32%


Pashtun_Afghan
Pashtun2_20Af
34.89%
8.45%
3.15%
7.05%
13.19%
0.00%
0.94%
1.29%
0.59%
16.59%
3.16%
1.77%
5.87%
3.07%


Pashtun_Afghan
Pashtun10_17Af
38.26%
8.48%
2.96%
7.38%
8.50%
0.10%
1.67%
0.44%
0.00%
13.07%
3.28%
8.35%
5.75%
1.75%


Pashtun_Afghan
Pashtun2_22Af
31.56%
3.83%
1.62%
19.43%
5.35%
0.06%
10.86%
0.96%
0.00%
8.53%
1.14%
13.76%
2.89%
0.00%


Pashtun_Afghan
Pashtun2_6Af
28.00%
5.94%
4.89%
4.59%
3.36%
0.32%
12.99%
2.18%
0.00%
10.00%
2.10%
12.54%
5.94%
7.16%


Pashtun_Afghan
Pashtun2_8Af
31.87%
10.13%
2.80%
11.39%
3.24%
0.73%
0.00%
7.73%
1.57%
12.15%
2.85%
11.56%
1.73%
2.26%


Pathan
HGDP00230
26.95%
5.69%
2.67%
5.29%
14.74%
0.00%
1.73%
0.00%
1.39%
32.28%
0.00%
9.24%
0.00%
0.02%


Pathan
HGDP00213
40.62%
3.46%
3.09%
8.08%
12.44%
0.00%
0.43%
0.00%
0.00%
23.07%
0.11%
5.76%
2.94%
0.00%


Pathan
HGDP00224
36.65%
1.89%
5.67%
6.72%
11.81%
0.00%
0.00%
4.49%
0.00%
19.26%
2.02%
5.68%
4.26%
1.54%


Pathan
HGDP00262
37.68%
1.22%
6.14%
8.86%
11.55%
0.00%
3.07%
2.70%
0.00%
22.66%
3.65%
2.47%
0.00%
0.00%


Pathan
HGDP00258
28.57%
7.59%
0.00%
8.10%
11.10%
0.00%
3.25%
0.00%
0.50%
29.72%
1.61%
4.67%
0.00%
4.88%


Pathan
HGDP00222
37.39%
5.70%
4.05%
2.40%
9.98%
1.89%
2.37%
0.34%
0.00%
29.89%
0.00%
3.12%
2.88%
0.00%


Pathan
HGDP00232
35.64%
4.51%
5.29%
3.08%
9.73%
0.00%
0.00%
1.26%
0.59%
30.60%
2.37%
2.57%
3.75%
0.62%


Pathan
HGDP00248
38.58%
5.27%
0.00%
8.27%
9.49%
0.87%
0.00%
3.36%
0.13%
20.79%
0.69%
3.58%
8.97%
0.00%

Tag Heuer
11-19-2015, 09:49 PM
I'll PM u a later today with instructions to get included in future projects

is it possible to include me as well?

Gravetto-Danubian
11-19-2015, 10:51 PM
IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


SATSURBILA
HL
80.50%
0.00%
10.40%
0.00%
0.00%
3.99%
0.00%
2.92%
2.18%
0.00%
0.00%
0.00%
0.00%
0.00%


RISE_baArm
RISE416
76.17%
0.00%
0.00%
0.00%
21.41%
0.00%
2.41%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%


KOTIAS
KK1
63.76%
7.24%
10.15%
5.65%
0.00%
0.00%
0.00%
1.00%
0.94%
0.00%
1.77%
6.37%
2.06%
1.06%


RISE_irArm
RISE408
59.62%
0.00%
21.50%
0.00%
18.88%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%
0.00%


Makrani
HGDP00158
59.39%
6.47%
3.60%
2.32%
0.00%
4.21%
0.00%
0.00%
0.00%
11.60%
2.63%
2.84%
6.94%
0.00%


Brahui
HGDP00025
57.62%
4.24%
0.00%
4.24%
3.76%
0.00%
2.30%
1.59%
0.73%
16.18%
7.44%
1.82%
0.00%
0.08%


Balochi
HGDP00086
56.18%
4.08%
0.00%
0.00%
6.54%
0.00%
0.00%
0.75%
0.00%
18.33%
9.82%
0.00%
1.47%
2.81%


Brahui
HGDP00045
55.18%
4.85%
0.00%
5.34%
2.76%
0.00%
4.58%
2.27%
0.57%
15.03%
9.42%
0.00%
0.00%
0.00%


Balochi
HGDP00052
53.96%
8.73%
0.00%
5.76%
1.61%
0.00%
0.00%
0.00%
0.00%
17.73%
6.51%
0.00%
4.75%
0.94%


Makrani
HGDP00148
53.67%
0.00%
1.37%
4.10%
7.84%
3.45%
0.00%
4.16%
1.49%
13.52%
4.44%
4.76%
0.00%
1.18%


Brahui
HGDP00033
53.20%
3.42%
0.00%
5.06%
0.93%
0.00%
0.16%
4.44%
0.00%
14.94%
7.45%
10.39%
0.00%
0.00%


Brahui
HGDP00005
53.02%
5.28%
0.00%
2.71%
6.47%
0.00%
1.52%
0.00%
0.00%
19.30%
6.07%
0.00%
4.77%
0.86%


Makrani
HGDP00151
52.13%
5.17%
3.41%
0.65%
0.00%
2.79%
0.39%
1.52%
0.02%
14.57%
13.51%
4.29%
1.56%
0.00%


Makrani
HGDP00131
52.02%
3.90%
2.80%
0.00%
3.72%
4.48%
3.50%
0.23%
0.00%
16.74%
4.84%
6.49%
0.00%
1.27%


Makrani
HGDP00133
52.01%
1.43%
2.00%
7.20%
1.27%
3.88%
0.00%
0.00%
1.04%
16.63%
2.62%
8.94%
0.00%
2.96%


Brahui
HGDP00007
51.98%
0.63%
2.71%
8.91%
0.46%
2.88%
0.00%
2.01%
0.00%
16.30%
3.27%
5.60%
0.00%
5.25%


Brahui
HGDP00011
51.58%
0.63%
0.00%
9.92%
0.25%
1.54%
0.00%
3.24%
0.39%
14.70%
7.44%
7.15%
0.00%
3.15%


Makrani
HGDP00135
51.33%
3.46%
2.44%
5.19%
6.83%
0.00%
0.64%
0.71%
0.88%
17.94%
6.24%
2.65%
0.00%
1.70%


Makrani
HGDP00134
51.05%
3.98%
3.04%
3.62%
1.58%
5.84%
0.00%
1.38%
1.09%
11.77%
10.86%
3.09%
2.71%
0.00%


Brahui
HGDP00023
50.79%
1.37%
6.10%
10.63%
0.72%
2.25%
0.00%
0.77%
0.24%
17.28%
7.50%
0.00%
0.00%
2.35%


Makrani
HGDP00137
50.69%
3.85%
0.00%
11.99%
5.25%
4.52%
1.40%
3.13%
0.00%
9.19%
5.60%
3.73%
0.63%
0.00%


Brahui
HGDP00003
50.56%
2.91%
3.37%
2.58%
0.00%
1.12%
0.42%
1.72%
0.05%
21.44%
1.48%
11.59%
2.72%
0.04%


Balochi
HGDP00080
50.49%
4.13%
2.31%
3.98%
1.62%
2.42%
0.00%
2.73%
0.01%
16.72%
6.62%
5.97%
0.00%
2.98%


Brahui
HGDP00043
49.94%
3.71%
1.52%
5.60%
2.04%
2.56%
3.11%
3.15%
0.49%
18.69%
8.69%
0.00%
0.00%
0.48%


Brahui
HGDP00017
49.94%
7.72%
0.00%
7.22%
1.69%
1.24%
0.68%
0.00%
0.64%
18.43%
3.64%
6.71%
2.10%
0.00%


Brahui
HGDP00001
49.73%
8.95%
3.12%
2.33%
3.07%
2.02%
7.31%
0.32%
0.00%
15.08%
8.08%
0.00%
0.00%
0.00%


Brahui
HGDP00035
49.57%
4.41%
2.75%
6.81%
0.00%
1.08%
9.59%
0.98%
0.00%
13.54%
7.98%
3.30%
0.00%
0.00%


Balochi
HGDP00064
49.35%
5.27%
3.30%
3.92%
0.46%
2.14%
0.00%
2.27%
0.00%
13.63%
13.76%
3.61%
0.00%
2.28%



Nice work, Kurd. How 'robust' are these findings ?
Im particularly interested in the BA_Armenian. Showing 0% Yamnaya, and 76% CHG and the rest WHG, it doesn't really support a steppic origin for BA Armenians, or their R1b, does it ?

Gravetto-Danubian
11-19-2015, 10:53 PM
Ok folks, I have finally been able to incorporate all 3 genomes into my dataset, Kotias, Bichon, and Satsurbila. My K14 transversions SNP based ADMIXTURE calculator is showing Kotias and Satsurbila very Gedrosian alligned, and Bichon quite similar to Loushbour. Balochis et al scored the highest CHG. Also, I was able to observe substructure within Yamnaya, where some were very EHG shifted. Here are results for a few members. More ADMIXTURE runs at various K to follow:



IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


.Awale
ID001
0.00%
0.00%
0.42%
0.00%
4.52%
43.75%
0.00%
0.00%
1.13%
0.00%
50.17%
0.00%
0.00%
0.00%


.Bol_Nat
ID001
31.99%
2.03%
7.21%
6.46%
4.77%
0.00%
0.00%
0.36%
0.90%
33.66%
3.55%
2.28%
3.69%
3.11%


.Bored
ID001
31.46%
4.25%
2.85%
6.54%
11.01%
0.00%
7.13%
0.80%
0.00%
33.33%
0.00%
0.00%
0.62%
2.01%


.Dluffy
ID001
34.02%
7.65%
0.76%
5.15%
9.35%
0.00%
2.38%
2.17%
2.14%
36.23%
0.00%
0.13%
0.00%
0.00%


.DMXX
ID001
34.02%
4.29%
2.45%
7.12%
2.96%
1.39%
5.84%
1.21%
1.04%
3.02%
17.43%
17.92%
0.00%
1.29%


.Farid
ID001
41.09%
5.85%
1.79%
8.86%
0.00%
3.44%
0.00%
1.63%
0.37%
14.80%
14.67%
4.78%
0.00%
2.72%


.Jesus
ID001
31.98%
5.04%
2.33%
13.55%
0.00%
2.80%
0.52%
2.66%
0.29%
9.72%
16.11%
12.98%
2.02%
0.00%


.Kandhari
ID001
38.71%
4.74%
11.09%
0.00%
7.23%
0.00%
1.85%
0.43%
0.00%
17.12%
4.21%
7.76%
0.39%
6.47%


.Kenji
ID001
20.66%
3.84%
3.49%
11.00%
10.21%
0.00%
0.00%
4.86%
0.00%
31.01%
3.75%
5.62%
5.55%
0.00%


.KURD
ID001
42.86%
2.35%
6.09%
1.46%
5.68%
2.03%
0.92%
1.68%
0.00%
22.99%
1.42%
3.75%
4.95%
3.83%


.Pak_Gujjar
ID001
35.11%
5.94%
0.00%
5.29%
4.99%
0.91%
0.00%
0.61%
1.40%
33.31%
0.00%
9.18%
2.98%
0.29%


.Passa
ID001
13.30%
0.00%
0.66%
6.57%
19.79%
0.00%
1.83%
1.63%
0.00%
0.00%
7.69%
48.52%
0.00%
0.00%


.Rukha
ID001
41.44%
8.34%
4.42%
1.46%
11.70%
1.04%
2.15%
4.74%
0.78%
15.68%
1.27%
4.48%
2.51%
0.00%


.Varun
ID001
25.04%
5.07%
1.02%
10.55%
0.47%
0.00%
2.71%
0.31%
0.25%
45.16%
0.00%
4.20%
0.00%
5.22%


.Zara
ID001
43.20%
7.37%
0.00%
13.30%
0.00%
4.88%
0.86%
2.61%
0.51%
7.94%
13.01%
5.48%
0.00%
0.85%


.Zephyrous
ID001
36.36%
5.73%
3.48%
2.83%
0.00%
0.00%
0.00%
2.86%
0.37%
1.50%
20.17%
25.71%
0.05%
0.93%


Abkhasian
abh119
48.92%
6.28%
1.34%
2.44%
0.79%
0.00%
2.40%
2.45%
0.65%
3.09%
0.47%
29.26%
0.00%
1.92%


Abkhasian
abh41
36.50%
3.16%
6.69%
7.35%
6.97%
0.17%
0.00%
2.83%
0.00%
2.26%
6.51%
26.51%
0.00%
1.04%


Abkhasian
abh147
37.32%
5.10%
5.12%
5.47%
4.01%
0.00%
1.02%
0.00%
0.00%
0.00%
3.80%
34.15%
3.11%
0.90%


Abkhasian
abh27
47.50%
2.39%
4.10%
0.00%
4.00%
1.67%
0.50%
4.07%
0.00%
0.00%
2.27%
30.26%
2.44%
0.80%


Abkhasian
abh24
40.59%
3.26%
4.05%
6.35%
0.26%
1.19%
2.56%
2.91%
0.69%
0.00%
3.57%
33.67%
0.47%
0.43%



Any data sets with Pashtuns, Gujarat, Iranians and some Europeans ?

Kurd
11-19-2015, 11:12 PM
Nice work, Kurd. How 'robust' are these findings ?
Im particularly interested in the BA_Armenian. Showing 0% Yamnaya, and 76% CHG and the rest WHG, it doesn't really support a steppic origin for BA Armenians, or their R1b, does it ?

The Allignment with Gedrosian pops should be pretty good for CHG, but I will be doing other ADMIXTURE runs to solidify. I anticipate using a couple of runs to put together a calculator for Gedmatch within the next week or two.

BA Armenians seem to be one of the most diverse ancient pops in my runs, so I would not necessarily take this one to be representative. Additional runs may help, but from what I have seen over the last few months is that the Caucuses area seems to have been crossroads where all kinds of diverse pops met. The time seperation between the BA Armenian samples probably accounts for some of this diversity

With regards to Iranians and Pashtuns check the beginning of this page

Gravetto-Danubian
11-19-2015, 11:39 PM
The Allignment with Gedrosian pops should be pretty good for CHG, but I will be doing other ADMIXTURE runs to solidify. I anticipate using a couple of runs to put together a calculator for Gedmatch within the next week or two.

BA Armenians seem to be one of the most diverse ancient pops in my runs, so I would not necessarily take this one to be representative. Additional runs may help, but from what I have seen over the last few months is that the Caucuses area seems to have been crossroads where all kinds of diverse pops met. The time seperation between the BA Armenian samples probably accounts for some of this diversity

With regards to Iranians and Pashtuns check the beginning of this page

Thanks
Yes no surprises that the south caucasus a cross roads
I find it odd that said sample has WHG but no EF.
Let's see what more tests show and what the other BA-Armenians show
Thanks

Chad Rohlfsen
11-20-2015, 12:51 AM
Nice work, Kurd. How 'robust' are these findings ?
Im particularly interested in the BA_Armenian. Showing 0% Yamnaya, and 76% CHG and the rest WHG, it doesn't really support a steppic origin for BA Armenians, or their R1b, does it ?

They're steppe and EEF shifted, from CHG. You'll see when I get the samples.

Kurd
11-20-2015, 01:39 AM
The Allignment with Gedrosian pops should be pretty good for CHG, but I will be doing other ADMIXTURE runs to solidify. I anticipate using a couple of runs to put together a calculator for Gedmatch within the next week or two.

BA Armenians seem to be one of the most diverse ancient pops in my runs, so I would not necessarily take this one to be representative. Additional runs may help, but from what I have seen over the last few months is that the Caucuses area seems to have been crossroads where all kinds of diverse pops met. The time seperation between the BA Armenian samples probably accounts for some of this diversity

With regards to Iranians and Pashtuns check the beginning of this page

I checked the age of the BA Armenian samples, and surprisingly they are not very much time separated. They all seem to be around 3000 years old. Therefore the diversity is more a function of populations of various backgrounds co-existing in the Caucuses in the Bronze Age rather than anything else.

RISE 397, 407, 412 show substantial Balkan farmer admixture (32 - 40%). RISE423, RISE407, RISE397, RISE412, RISE413 all show substantial Yamnaya shared ancestry (ADMIXTURE does not convey direction of genflow, although I suspect that RISE 412, 413, and 423 have steppe input due to them showing substantial EHG specific admixture). It looks like there was geneflow both into and from the steppe in the Caucuses.

ZephyrousMandaru
11-20-2015, 01:57 AM
Kurd, are you planning on releasing a new calculator? If so, any idea why there isn't a Southwest Asian or EEF component?

Gravetto-Danubian
11-20-2015, 02:08 AM
I checked the age of the BA Armenian samples, and surprisingly they are not very much time separated. They all seem to be around 3000 years old. Therefore the diversity is more a function of populations of various backgrounds co-existing in the Caucuses in the Bronze Age rather than anything else.

RISE 397, 407, 412 show substantial Balkan farmer admixture (32 - 40%). RISE423, RISE407, RISE397, RISE412, RISE413 all show substantial Yamnaya shared ancestry (ADMIXTURE does not convey direction of genflow, although I suspect that RISE 412, 413, and 423 have steppe input due to them showing substantial EHG specific admixture). It looks like there was geneflow both into and from the steppe in the Caucuses.

I think as one would expect from the archaeological evidence.

Can you give us an idea of the figures ?

Arbogan
11-20-2015, 02:19 AM
Kurd, are you planning on releasing a new calculator? If so, any idea why there isn't a Southwest Asian or EEF component?

You should look again. Balkan farmer: ENF. East-African: South-west Asian.

Kurd
11-20-2015, 03:16 AM
Kurd, are you planning on releasing a new calculator? If so, any idea why there isn't a Southwest Asian or EEF component?

Yes, within 2 weeks. It will be a k14 - K16 with SW Asian, EF, CHG, WHG, E/W African, and a few other Eurasian comps

MonkeyDLuffy
11-20-2015, 07:20 AM
Ok folks, I have finally been able to incorporate all 3 genomes into my dataset, Kotias, Bichon, and Satsurbila. My K14 transversions SNP based ADMIXTURE calculator is showing Kotias and Satsurbila very Gedrosian alligned, and Bichon quite similar to Loushbour. Balochis et al scored the highest CHG. Also, I was able to observe substructure within Yamnaya, where some were very EHG shifted. Here are results for a few members. More ADMIXTURE runs at various K to follow:



IND
ID001
Caucusus HG
EHG
Yamanya
Kalash
WHG
W_African
SE_Asian
Onge
Archaic_Human
Paniya
E_African
Balkan NF
E_Asian
Siberian


.Awale
ID001
0.00%
0.00%
0.42%
0.00%
4.52%
43.75%
0.00%
0.00%
1.13%
0.00%
50.17%
0.00%
0.00%
0.00%


.Bol_Nat
ID001
31.99%
2.03%
7.21%
6.46%
4.77%
0.00%
0.00%
0.36%
0.90%
33.66%
3.55%
2.28%
3.69%
3.11%


.Bored
ID001
31.46%
4.25%
2.85%
6.54%
11.01%
0.00%
7.13%
0.80%
0.00%
33.33%
0.00%
0.00%
0.62%
2.01%


.Dluffy
ID001
34.02%
7.65%
0.76%
5.15%
9.35%
0.00%
2.38%
2.17%
2.14%
36.23%
0.00%
0.13%
0.00%
0.00%


.DMXX
ID001
34.02%
4.29%
2.45%
7.12%
2.96%
1.39%
5.84%
1.21%
1.04%
3.02%
17.43%
17.92%
0.00%
1.29%


.Farid
ID001
41.09%
5.85%
1.79%
8.86%
0.00%
3.44%
0.00%
1.63%
0.37%
14.80%
14.67%
4.78%
0.00%
2.72%


.Jesus
ID001
31.98%
5.04%
2.33%
13.55%
0.00%
2.80%
0.52%
2.66%
0.29%
9.72%
16.11%
12.98%
2.02%
0.00%


.Kandhari
ID001
38.71%
4.74%
11.09%
0.00%
7.23%
0.00%
1.85%
0.43%
0.00%
17.12%
4.21%
7.76%
0.39%
6.47%


.Kenji
ID001
20.66%
3.84%
3.49%
11.00%
10.21%
0.00%
0.00%
4.86%
0.00%
31.01%
3.75%
5.62%
5.55%
0.00%


.KURD
ID001
42.86%
2.35%
6.09%
1.46%
5.68%
2.03%
0.92%
1.68%
0.00%
22.99%
1.42%
3.75%
4.95%
3.83%


.Pak_Gujjar
ID001
35.11%
5.94%
0.00%
5.29%
4.99%
0.91%
0.00%
0.61%
1.40%
33.31%
0.00%
9.18%
2.98%
0.29%


.Passa
ID001
13.30%
0.00%
0.66%
6.57%
19.79%
0.00%
1.83%
1.63%
0.00%
0.00%
7.69%
48.52%
0.00%
0.00%


.Rukha
ID001
41.44%
8.34%
4.42%
1.46%
11.70%
1.04%
2.15%
4.74%
0.78%
15.68%
1.27%
4.48%
2.51%
0.00%


.Varun
ID001
25.04%
5.07%
1.02%
10.55%
0.47%
0.00%
2.71%
0.31%
0.25%
45.16%
0.00%
4.20%
0.00%
5.22%


.Zara
ID001
43.20%
7.37%
0.00%
13.30%
0.00%
4.88%
0.86%
2.61%
0.51%
7.94%
13.01%
5.48%
0.00%
0.85%


.Zephyrous
ID001
36.36%
5.73%
3.48%
2.83%
0.00%
0.00%
0.00%
2.86%
0.37%
1.50%
20.17%
25.71%
0.05%
0.93%


Abkhasian
abh119
48.92%
6.28%
1.34%
2.44%
0.79%
0.00%
2.40%
2.45%
0.65%
3.09%
0.47%
29.26%
0.00%
1.92%


Abkhasian
abh41
36.50%
3.16%
6.69%
7.35%
6.97%
0.17%
0.00%
2.83%
0.00%
2.26%
6.51%
26.51%
0.00%
1.04%


Abkhasian
abh147
37.32%
5.10%
5.12%
5.47%
4.01%
0.00%
1.02%
0.00%
0.00%
0.00%
3.80%
34.15%
3.11%
0.90%


Abkhasian
abh27
47.50%
2.39%
4.10%
0.00%
4.00%
1.67%
0.50%
4.07%
0.00%
0.00%
2.27%
30.26%
2.44%
0.80%


Abkhasian
abh24
40.59%
3.26%
4.05%
6.35%
0.26%
1.19%
2.56%
2.91%
0.69%
0.00%
3.57%
33.67%
0.47%
0.43%



What is EHG kurd? Something Siberian?

DMXX
11-20-2015, 09:54 AM
What is EHG kurd? Something Siberian?

Eastern Hunter-Gatherer (EHG) is a distinct component that was picked up in Eastern Europe by Haak et al.. It manifested itself through the Samara and Karelia HG genomes. Yamnaya has been consistently demonstrated to be at least half EHG by both researchers and Davidski.

All of us are operating with a large degree of uncertainty regarding the nature of this component in Asia. I've stated my own view several times (suspect there was continuous gene flow from the steppes into SC Asia since the paleolithic via HG groups), but the material evidence is sparse and we require aDNA from SC Asia before scenarios can be validated against one another.

I'm somewhat confused regarding the presence of a "Yamnaya" component here, when Yamnaya should (as per Jones et al.) be considered a hybridisation of EHG and CHG.

Gravetto-Danubian
11-20-2015, 10:48 AM
U


I'm somewhat confused regarding the presence of a "Yamnaya" component here, when Yamnaya should (as per Jones et al.) be considered a hybridisation of EHG and CHG.

Same here
If Kurd's Calculator has an "EHG" and a "CHG"; as well as Balkan farmer; where's an additional/ residual "Yamnaya" coming from ?

:)

Arbogan
11-20-2015, 11:28 AM
I'm thinking it's to differentate between steppe related EHG and general EHG. Whether any EHG remained significantly non steppe related is an important question.

Kurd
11-20-2015, 12:11 PM
Eastern Hunter-Gatherer (EHG) is a distinct component that was picked up in Eastern Europe by Haak et al.. It manifested itself through the Samara and Karelia HG genomes. Yamnaya has been consistently demonstrated to be at least half EHG by both researchers and Davidski.

All of us are operating with a large degree of uncertainty regarding the nature of this component in Asia. I've stated my own view several times (suspect there was continuous gene flow from the steppes into SC Asia since the paleolithic via HG groups), but the material evidence is sparse and we require aDNA from SC Asia before scenarios can be validated against one another.

I'm somewhat confused regarding the presence of a "Yamnaya" component here, when Yamnaya should (as per Jones et al.) be considered a hybridisation of EHG and CHG.

For the benefit of those with not as a good an understanding of the concepts, DMXX's point, which is valid, is that if Yamnaya is a hybridized product of EHG and CHG, then why does ADMIXTURE show a Yamnaya percentage in the parent, namely, CHG.

An example, illustrated by a somewhat similar situation may help a little in this regard. Let's look at the Kalash and the Baloch. ADMIXTURE shows both to be a mix of Caucasian and S Asian, yet when they are allowed to form their own modal component in ADMIXTURE, Caucasians show a percentage of Baloch, and a percentage of Kalash, even though it is unlikely that most Caucasians have any direct Kalash or Baloch ancestry.

Just focusing on the Kalash for a minute, they appear to be a majority Caucasian (likely CHG) and minority S Asian in ADMIXTURE, yet ADMIXTURE shows individuals from populations from all over W Eurasia as having a Kalash percentage, even though in all likelihood most are not descended from Kalash. So whether ADMIXTURE is picking up on stretches in the genome that have the same mix ratios of alleles as the Kalash, or whether it is picking up loci that have a Kalash/Caucasian overlapping allele frequency, I am not sure about.

The same situation is probably manifesting itself here, although I believe it will be magnified in a parent, versus someone much more distantly related

alan
11-20-2015, 12:12 PM
I imagine we will discover a few more of these pockets of hunters in SW Asia - only some of which were involved in the first farming waves but which were close enough to have had some input into Europe at some point. I think we have indirectly seen that the western half of Turkey probably had WHG type people before the farming expansion but there are several hunter groups to be defined. I suspect the hunters in the southern part of the Levant will be E people. We dont know the genetics of the Zarzian group of the north Zagros area as yet. We dont know yet what the south Caspian coast hunter-fishers were genetically or the Keltiminar east Caspian hunters. There are all sorts of hunter groups in the Stans and Siberia in the Mesolithic we have no idea about. There are several less well known hunter groups too around the Caucasus. So, we may find a few more components. Ultimately all groups go back to hunters until the Younger Dryas so in deep time terms the distinction between hunters and farmers is somewhat wrongheaded.

alan
11-20-2015, 12:20 PM
For the benefit of those with not as a good an understanding of the concepts, DMXX's point, which is valid, is that if Yamnaya is a hybridized product of EHG and CHG, then why does ADMIXTURE show a Yamnaya percentage in the parent, namely, CHG.

An example, illustrated by a somewhat similar situation may help a little in this regard. Let's look at the Kalash and the Baloch. ADMIXTURE shows both to be a mix of Caucasian and S Asian, yet when they are allowed to form their own modal component in ADMIXTURE, Caucasians show a percentage of Baloch, and a percentage of Kalash, even though it is unlikely that most Caucasians don't have any direct Kalash or Baloch ancestry.

Just focusing on the Kalash for a minute, they appear to be a majority Caucasian (likely CHG) and minority S Asian in ADMIXTURE, yet ADMIXTURE shows individuals from populations from all over W Eurasia as having a Kalash percentage, even though in all likelihood most are not descended from Kalash. So whether ADMIXTURE is picking up on stretches in the genome that have the same mix of alleles as the Kalash, or whether it is picking up loci that have a Kalash/Caucasian overlapping allele frequency, I am not sure about.

The same situation is probably manifesting itself here.

I think its because EHG is a hybrid of Paelaeolithic WHG types and Mesolithic arrivals from the east carrying ANE. If you go back far enough IMO it will be seen that ANE operated individually from ANE until the two hybrided at some point in the end of the Palaeolithic in the steppe, NE Europe and the north of SW Asia. However some ANE groups who had not hybrided with WHG would have continued to exist and spread. ANE groups could have formed a number of hybrid with existing hunter groups wherever they went. Presumably when ANE arrived in the north of SW Asia and central Asia they formed hybrids other than EHG. I feel the obvious conclusion that EHG is a hybrid of ANE and something like a drifted version of WHG is being ignored for Eurocentric reasons. Yes its not a perfect mathematic fit but how could that be expected when ANE groups had 10000 years to drift after Ma'lta and indeed some WHG groups may have been drifted too. Note too that Afontova Gora was also ANE and he was post-LGM. So, he is an example of how ANE must have remained in refugia - probably primarily Altai, drifting for 10000 years during the LGM before spreading out west and east. There could have been other ANE refugia but Altai is the obvious one.

Shaikorth
11-20-2015, 12:24 PM
Eastern Hunter-Gatherer (EHG) is a distinct component that was picked up in Eastern Europe by Haak et al.. It manifested itself through the Samara and Karelia HG genomes. Yamnaya has been consistently demonstrated to be at least half EHG by both researchers and Davidski.

All of us are operating with a large degree of uncertainty regarding the nature of this component in Asia. I've stated my own view several times (suspect there was continuous gene flow from the steppes into SC Asia since the paleolithic via HG groups), but the material evidence is sparse and we require aDNA from SC Asia before scenarios can be validated against one another.

I'm somewhat confused regarding the presence of a "Yamnaya" component here, when Yamnaya should (as per Jones et al.) be considered a hybridisation of EHG and CHG.

These hybridization theories are based on formal testing (f/d-stats, treemix etc.) and not ADMIXTURE. ADMIXTURE forms components based on the number and homogenuity of samples, and can't predict the direction of gene flow. MA-1 shows up in all the Reich lab paper ADMIXTURE runs as having Native American admixture while Native Americans always are 100% Native American, while formal tests will show it's actually the opposite.

alan
11-20-2015, 12:40 PM
Apparently the Zarzian probably arose from the Aurignacian of the same general area. So, some largely basal derived signal seems likely to me but probably distinctive due to isolation in the LGM. The area of course was at the eastern edge of the farming core too. It would be interesting to know what these eastern hunters at the eastern part of the early farming core carried and if it contrasted with the Tauros western side of this zone. I strongly suspect that the G dominance in the farmers who headed through Anatolia and into Europe must reflect origins in the hunter-turning into farmers in the Tauros west side of the early farming zone. However it may be complex because farming didnt spread into western half of Anatolia until thousands of years after the earliest moves towards farming arose in east Anatolia.

MonkeyDLuffy
11-20-2015, 06:10 PM
Eastern Hunter-Gatherer (EHG) is a distinct component that was picked up in Eastern Europe by Haak et al.. It manifested itself through the Samara and Karelia HG genomes. Yamnaya has been consistently demonstrated to be at least half EHG by both researchers and Davidski.

All of us are operating with a large degree of uncertainty regarding the nature of this component in Asia. I've stated my own view several times (suspect there was continuous gene flow from the steppes into SC Asia since the paleolithic via HG groups), but the material evidence is sparse and we require aDNA from SC Asia before scenarios can be validated against one another.

I'm somewhat confused regarding the presence of a "Yamnaya" component here, when Yamnaya should (as per Jones et al.) be considered a hybridisation of EHG and CHG.

We have same CHG, turan R brotherhood.

Place your brofist here.

DMXX
11-20-2015, 07:25 PM
We have same CHG, turan R brotherhood.

Place your brofist here.

Matched CHG for all to see,
Though its position is uncertain in phylogeny;
Y-DNA R bro's keep the Mal'ta crew alive,
A brofist it'll have to be;
Pizza fingers man, no hi-fives

(Before you guys and gals mass-report this message, just know it sounded amazing in my head)