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Xehanort
09-23-2017, 04:35 AM
Hi everyone, there was a recent DNA study comparing modern Iranians and Iranian Zoroastrians, and it turns out and modern Iranians are completely different from their ancestors. There is significant evidence that suggests that modern Iranians have elevated Middle Eastern and South Asian ancestry, and in the case of the Bandaris, African ancestry.

Source (can't post link), look up: The Genetic Legacy of Zoroastrianism in Iran and India: Insights into Population Structure, Gene Flow, and Selection (Science Direct)

Genetiker's analysis of the Genomes, source (scroll down to see the comparisons): Genetiker, Ancient Egyptian K = 14 Analysis (scroll down to see the Iranian samples).

RCO
09-23-2017, 09:43 AM
Just like in any people. We need to understand the differences. We still don't have any comprehensive study about Ancient Iranians or even modern Iranians. What were the Ancient Iranian specific Y-DNA clusters, mtDNA and atDNA. There's a big gap in the investigation and we need more ancient samples because Iran was a central hub of the Eurasian demographic transformations. I think I could discover at least one of the Ancient Iranian Y-DNA J1 lines in my investigations J1-FGC6064 and downstream SNPs are completely different from other regions but we need NGS of specific Iranian J2, R1a, G, L types born in Iran in the last thousand years and different from the Turkic, Mongolian, Arabic, Caucasian, Slavic or Indic clusters.

Xehanort
09-23-2017, 03:55 PM
Well, the study found that the Y-DNA was mainly the same, Haplogroup J2 was the majority. There are some variations in the MtDNA, but overall that looks stable as well. The difference here is just that modern Iranians have reduced Neolithic Iranian genes, mainly due to mixing with Turks.

RCO
09-23-2017, 05:28 PM
I think they had important changes. It's important to find what were or are the possible specific Iranian Y-DNA clusters because they have spatial and temporal structures related mainly to Iranian populations. We can observe the Y-DNA SNPs only associated or mainly concentrated within the Iranian populations, just like we can find what are the clusters and SNPs usually associated to any other existing ethno-historical groups. Others arrived, migrated or invaded Iran from other places and they also match with non-Iranian clusters from other regions and cultures not primarily or exclusively associated with the Ancient Iranian Peoples. The problem here is nobody has ever made a good article about NGS Iranian Y-DNA. What are the possible Iranian J2, J1, R1a, L, G ethno-historical clusters found primarily and exclusively in Iranian populations and different from Turkic, Mongolian, Arabic, Caucasian, Slavic or Indic clusters ?

Xehanort
09-23-2017, 10:33 PM
I am not sure, to be honest. However, I think the Iranian gene pool has remained stable for the same part, and I am not denying that. All I am saying is that modern Iranians have increased non-Iranian ancestry than the Zoroastrians, mainly from Turks, but also from Middle Easterners and South Asians. I would say that Iranians are still 50 to 85% the same as their ancestors. Until we find an Achaemenid or Sassanid sample which is adequate for DNA testing, we cannot conclusively determine the amount of non-Iranic ancestry in Iranians.

StarDS9
09-26-2017, 06:50 PM
The ancient Iranians that had settled Iran were not pure North European like people. The Indo-Iranians had settled in what is known as BMAC region in Central Asia where they mixed with a much larger population. By the time they made to Iran these Ancient iranians(Ancestors of Persians,Medes) were heavly Central South Asian like with some North Euro. Modern day Iranians like Persians and Kurds both show a shift towards Central Asia then any other groups in the Middle-East. Also by the time of the Parthians, Iranians had already Iranized all the native population.

I believe 20-30% of modern day Iranian ancestry comes from the Iranians that came from the BMAC Iranians.

DMXX
10-03-2017, 05:10 AM
Per formal stats (e.g. qpAdm), modern Iranians are predominantly Chalcolithic and Neolithic Iranian farmer (usually over 70%). The next largest component is Late Neolithic Bronze Age ancestry from the Eurasian steppes (over 15%). Additionally, most modern Iranians are over 70% similar to the Iron Age Iranian from NW Iran (Hasanlu Tepe, south of Urmia). That is in spite of the apparent prehistoric regional differences in autochthonous ancestry (southern Iranians seem to have a surplus in quasi-ASI-Iran_N-type ancestry, whereas the north has more EEF).

Therefore, modern Iranians certainly aren't ancient Iranians, but there is a remarkable degree of continuity from the Chalcolithic onwards (contrast this with the stark difference in autosomal profile between the Neolithic Stuttgart genome and modern Germans). We can also be quite certain the bulk of that difference is through a surplus in pre-Turkish Indo-European steppe heritage. We also do not need Achaemanid or Sassanid aDNA to arrive at these conclusions, as we have an Iron Age Iranian sample that comfortably approximates the majority of the heritage of most Iranians.

The main difference between the Iron Age Iranian and modern Iranians from around that vicinity is that the latter tend to have more LNBA steppe heritage. However, we do not know much about the socio-linguistic position of this individual. He existed just before the Median empire was established. We also do not know how typical he was of his era. Ergo, the nature of the inflated LNBA steppe in modern NW Iranians relative to him is uncertain at this point.

The difference highlighted between Zoroastrians and other Iranians represents regional differences in ancestry for the most part. The general trajectory of difference between Zoroastrians from Yazd versus Mazandaranis and other northern Iranians is akin to that shared between the latter groups and other southern Iranian populations. The additional non-plateau ancestry in non-Zoroastrian Iranians (either East Eurasian or Sub-Saharan) looks to be about 0-5% in the majority.

As a penultimate closing comment, we have read speculation (usually from non-Iranians) for years that modern Iranians are substantially different from their ancient ancestors through non-plateau admixture. We can now disregard that oft-repeated assumption with quantifiable evidence.

The final closing comment relates to the Kurds (particularly the Kurmanji) - We can consider them to be NW Iranians from a genetic standpoint for all intents and purposes, permitting us to include them in the points above concerning NW Iranians.

Xehanort
10-06-2017, 08:29 AM
Per formal stats (e.g. qpAdm), modern Iranians are predominantly Chalcolithic and Neolithic Iranian farmer (usually over 70%). The next largest component is Late Neolithic Bronze Age ancestry from the Eurasian steppes (over 15%). Additionally, most modern Iranians are over 70% similar to the Iron Age Iranian from NW Iran (Hasanlu Tepe, south of Urmia). That is in spite of the apparent prehistoric regional differences in autochthonous ancestry (southern Iranians seem to have a surplus in quasi-ASI-Iran_N-type ancestry, whereas the north has more EEF).

Therefore, modern Iranians certainly aren't ancient Iranians, but there is a remarkable degree of continuity from the Chalcolithic onwards (contrast this with the stark difference in autosomal profile between the Neolithic Stuttgart genome and modern Germans). We can also be quite certain the bulk of that difference is through a surplus in pre-Turkish Indo-European steppe heritage. We also do not need Achaemanid or Sassanid aDNA to arrive at these conclusions, as we have an Iron Age Iranian sample that comfortably approximates the majority of the heritage of most Iranians.

The main difference between the Iron Age Iranian and modern Iranians from around that vicinity is that the latter tend to have more LNBA steppe heritage. However, we do not know much about the socio-linguistic position of this individual. He existed just before the Median empire was established. We also do not know how typical he was of his era. Ergo, the nature of the inflated LNBA steppe in modern NW Iranians relative to him is uncertain at this point.

The difference highlighted between Zoroastrians and other Iranians represents regional differences in ancestry for the most part. The general trajectory of difference between Zoroastrians from Yazd versus Mazandaranis and other northern Iranians is akin to that shared between the latter groups and other southern Iranian populations. The additional non-plateau ancestry in non-Zoroastrian Iranians (either East Eurasian or Sub-Saharan) looks to be about 0-5% in the majority.

As a penultimate closing comment, we have read speculation (usually from non-Iranians) for years that modern Iranians are substantially different from their ancient ancestors through non-plateau admixture. We can now disregard that oft-repeated assumption with quantifiable evidence.

The final closing comment relates to the Kurds (particularly the Kurmanji) - We can consider them to be NW Iranians from a genetic standpoint for all intents and purposes, permitting us to include them in the points above concerning NW Iranians.

Thanks for replying. So basically, modern Iranians are pretty much the same with minor variations in their genetic composition. I think the African ancestry is usually no more than 1%, but many also have 0%. I was wondering, though, why is there a bit of a difference between Ancient and Modern Iranians, despite the genetic continuity of 70%? Thanks.

Xehanort
10-06-2017, 08:30 AM
The ancient Iranians that had settled Iran were not pure North European like people. The Indo-Iranians had settled in what is known as BMAC region in Central Asia where they mixed with a much larger population. By the time they made to Iran these Ancient iranians(Ancestors of Persians,Medes) were heavly Central South Asian like with some North Euro. Modern day Iranians like Persians and Kurds both show a shift towards Central Asia then any other groups in the Middle-East. Also by the time of the Parthians, Iranians had already Iranized all the native population.

I believe 20-30% of modern day Iranian ancestry comes from the Iranians that came from the BMAC Iranians.

Thanks, I appreciate it.

Batroun
10-06-2017, 08:41 PM
The ancient Iranians that had settled Iran were not pure North European like people. The Indo-Iranians had settled in what is known as BMAC region in Central Asia where they mixed with a much larger population. By the time they made to Iran these Ancient iranians(Ancestors of Persians,Medes) were heavly Central South Asian like with some North Euro. Modern day Iranians like Persians and Kurds both show a shift towards Central Asia then any other groups in the Middle-East. Also by the time of the Parthians, Iranians had already Iranized all the native population.

I believe 20-30% of modern day Iranian ancestry comes from the Iranians that came from the BMAC Iranians.

So the whole Indo-European genetic identity is really over exaggerated when it comes to modern day Farsi speaking Persian/Iranians?

Lupus82
10-06-2017, 09:26 PM
So the whole Indo-European genetic identity is really over exaggerated when it comes to modern day Farsi speaking Persian/Iranians?

In terms of Y-DNA haplogroup it is not that much exaggerated. Around 20% of the Persians (The haplogroup R1a) are direct descendants of the Indo-Iranian tribes migrated to Iran. This figure goes higher up as you go eastwardly towards Afghanistan and Tajikistan.

When it comes to autosomal DNA, the data indicates to more native ancestry.

Batroun
10-06-2017, 10:38 PM
In terms of Y-DNA haplogroup it is not that much exaggerated. Around 20% of the Persians (The haplogroup R1a) are direct descendants of the Indo-Iranian tribes migrated to Iran. This figure goes higher up as you go eastwardly towards Afghanistan and Tajikistan.

When it comes to autosomal DNA, the date indicates to more native ancestry.

So who autosomaly speaking really descends from these Indo-European peoples in that region of the world?

vatan
10-07-2017, 03:31 AM
So who autosomaly speaking really descends from these Indo-European peoples in that region of the world?

Mostly east iranics such as, the Tajik Pamiris, yaghnobis, and pashtuns. They have 40-70% ancestry from them.

West iranics have 10-25%.

MonkeyDLuffy
10-07-2017, 04:47 AM
Mostly east iranics such as, the Tajik Pamiris, yaghnobis, and pashtuns. They have 40-70% ancestry from them.

West iranics have 10-25%.

You mean the CHG %age?

ancestryfan1994
10-07-2017, 09:53 PM
There hasn't been any full scale analysis of modern Iranians compared to their counterparts from the past as far as im aware, which isn't much anyway so maybe i missed something. From what I've read here and there, its very likely that the Iranian gene pool remained pretty much the same since the bronze age, with the exception of a bit of turkic/SSA in more recent times though.

Lupus82
10-08-2017, 11:54 AM
There hasn't been any full scale analysis of modern Iranians compared to their counterparts from the past as far as im aware, which isn't much anyway so maybe i missed something. From what I've read here and there, its very likely that the Iranian gene pool remained pretty much the same since the bronze age, with the exception of a bit of turkic/SSA in more recent times though.

Where did this SSA come from? Was there extensive slave trade in Persia?

Also I find it odd that the Kurds have higher amount of European admixture than Persians do have. Because Persians are closer to the geographic homeland of the Aryan settlements.

RCO
10-08-2017, 01:20 PM
In terms of Y-DNA haplogroup it is not that much exaggerated. Around 20% of the Persians (The haplogroup R1a) are direct descendants of the Indo-Iranian tribes migrated to Iran. This figure goes higher up as you go eastwardly towards Afghanistan and Tajikistan.


What are the Iranian R1a clusters ? You can try to show the specific branches in YFull tree ?

Lupus82
10-08-2017, 02:11 PM
What are the Iranian R1a clusters ? You can try to show the specific branches in YFull tree ?

I believe they are generally under the subclades of R1a - Z93

ancestryfan1994
10-08-2017, 06:31 PM
Where did this SSA come from? Was there extensive slave trade in Persia?

Also I find it odd that the Kurds have higher amount of European admixture than Persians do have. Because Persians are closer to the geographic homeland of the Aryan settlements.

I can't say for sure, but SSA exists mostly in the south, and could have come from a number of sources. I think there was a slave trade in Iran, you can see the remnants of this through the Afro Iranian community that still exists in Khuzestan and surrounding areas today.

It could also come through contact with Arabs, like in my families case the 1-2% SSA is probably due to our Egyptian ancestry.

ADW_1981
10-08-2017, 06:33 PM
I am not sure, to be honest. However, I think the Iranian gene pool has remained stable for the same part, and I am not denying that. All I am saying is that modern Iranians have increased non-Iranian ancestry than the Zoroastrians, mainly from Turks, but also from Middle Easterners and South Asians. I would say that Iranians are still 50 to 85% the same as their ancestors. Until we find an Achaemenid or Sassanid sample which is adequate for DNA testing, we cannot conclusively determine the amount of non-Iranic ancestry in Iranians.

What you are calling "Iranian" is Middle Eastern. What are you on about?

RCO
10-08-2017, 09:50 PM
I believe they are generally under the subclades of R1a - Z93

Yes, quite obvious but we still don't have any Iranian detailed specific cluster and we don't know what kind of Iranian R1a clusters in Iran are different from Armenians, Central Asians, Indians, Turks, Slavs, Mongols and Arabs. If we had a good number of Iranian NGS we would be able to understand when they arrived in Iran and how they settled and could split and grow there, but as I said we still don't have data and we still can't formulate any idea about Indo-Europeanization of Iran via any haplogroup.

Xehanort
10-08-2017, 11:21 PM
So the whole Indo-European genetic identity is really over exaggerated when it comes to modern day Farsi speaking Persian/Iranians?

It is, indeed. The same can be said about Indians. Although, Y-Haplogroups tell us otherwise. But I think autosomally it is exaggerated.

Xehanort
10-08-2017, 11:26 PM
There hasn't been any full scale analysis of modern Iranians compared to their counterparts from the past as far as im aware, which isn't much anyway so maybe i missed something. From what I've read here and there, its very likely that the Iranian gene pool remained pretty much the same since the bronze age, with the exception of a bit of turkic/SSA in more recent times though.

Not much SSA at all, many Iranians don't have SSA, but a few from the very south (not Fars but Bander Abbas etc.) have significant African ancestry (4 to 20%). Also, Tehranis do seem to have a bit as well because slave women were imported into Qajar Iran from Africa and mainly concentrated in and around Tehran.

Iranians have more South Asian admixture (4 to 10%) than they do SSA (1 to 5%).

Xehanort
10-08-2017, 11:28 PM
Where did this SSA come from? Was there extensive slave trade in Persia?

Also I find it odd that the Kurds have higher amount of European admixture than Persians do have. Because Persians are closer to the geographic homeland of the Aryan settlements.

Iranians don't have SSA at all, but some in the South do, but Iranians from Fars don't, mainly those from Khuzistan and Bandaris do. It came from the Portuguese and the Qajar era slave trade. But I think it's safe to say that any distinguishable African ancestry is not present in at least 75% of Iranians!

Xehanort
10-08-2017, 11:30 PM
I can't say for sure, but SSA exists mostly in the south, and could have come from a number of sources. I think there was a slave trade in Iran, you can see the remnants of this through the Afro Iranian community that still exists in Khuzestan and surrounding areas today.

It could also come through contact with Arabs, like in my families case the 1-2% SSA is probably due to our Egyptian ancestry.

It's definitely due to your Egyptian ancestry. What percentage Egyptian are you? Most Egyptians are between 14 and 21% SSA.

Xehanort
10-08-2017, 11:31 PM
What you are calling "Iranian" is Middle Eastern. What are you on about?

Yes, but Iranians are genetically closer to populations from the Caucasus than they are to Middle Easterners from Arabia, Syria, the Levant, and even Anatolia. By Middle Eastern, I obviously meant non-Iranian.

Kurd
10-09-2017, 02:34 AM
I thought I'd share a couple of ChromoPainter heat maps that I ran for one of my projects. The matrix is based on the number of haplotypes shared between 2 samples. Analyzing with shared haplotypes is more robust than allele frequency analysis (for ex 23andMe uses haplotypes)

Blue indicates the highest number of shared haplotypes while yellow the lowest. As has been mentioned here Kurds and Iranians are almost indistinguishable genetically, that is why you see Kurds (Kurd F= Feyli Kurds, Kurd C=Kurmanji Kurds) sharing the maximum number of haplotypes (Blue) with Mazendarani Iranians, Zoroastrians, and Diploid Satsurbila. Iran N is underestimated because it is the haploid genome published by Lazaridis. I haven't had the time to process it for diploid genotypes yet. Once I do, its sharing will increase with some populations from Kurdistan to Pakistan.

The matrices also contain Caucasians, Europeans and ancient steppe samples that were imputed by Martiniano. The ones marked diploid, I processed and genotyped.

I have removed a large number of markers in linkage disequilibrium from the dataset


https://i.imgur.com/qeE0lty.png

https://i.imgur.com/bmCU1sK.png

ancestryfan1994
10-09-2017, 03:41 AM
It's definitely due to your Egyptian ancestry. What percentage Egyptian are you? Most Egyptians are between 14 and 21% SSA.

It ranges from 6-8%

Zoran
10-09-2017, 04:52 PM
Of course not, I am from West Iran have around 80% adna continuity with Iran_CHL (used one of those Eurogenes K36 tools to determine), the rest is Anatolian farmer and some N. Euro admixture (that came in later with the Indo-Iranian migrations), so modern Iranians are obviously not the same as Ancient Iranians but they are close.

Lupus82
10-09-2017, 05:35 PM
Of course not, I am from West Iran have around 80% adna continuity with Iran_CHL (used one of those Eurogenes K36 tools to determine), the rest is Anatolian farmer and some N. Euro admixture (that came in later with the Indo-Iranian migrations), so modern Iranians are obviously not the same as Ancient Iranians but they are close.

Would you post your result with regard to Iran CHL? I am Kurd from Turkey. I wish to compare your results with mine.

Zoran
10-09-2017, 06:44 PM
Would you post your result with regard to Iran CHL? I am Kurd from Turkey. I wish to compare your results with mine.

I1661 - Iran_CHL:


Admix Results (sorted):

# Population Percent
1 West_Asia 60.43
2 SW_Asia 14.44
3 SW_Europe 13.32
4 South_Asia 9.75
5 South_Africa 0.76
6 Oceania 0.44
7 East_Africa 0.35
8 Americas 0.27
9 SE_Asia 0.23

My results:

Admix Results (sorted):

# Population Percent
1 West_Asia 45.62
2 SW_Europe 21.19
3 SW_Asia 15.51
4 NE_Europe 6.86
5 South_Asia 6.07
6 NE_Asia 1.6
7 East_Africa 0.93
8 Americas 0.93
9 Siberia 0.56
10 South_Africa 0.55
11 West_Africa 0.2

https://i.imgur.com/YGKrePe.png

Use this website for comparison and post a screenshot like I did, would be nice:

http://gen3553.pagesperso-orange.fr/ADN/ancient.htm

Xehanort
10-09-2017, 07:04 PM
I thought I'd share a couple of ChromoPainter heat maps that I ran for one of my projects. The matrix is based on the number of haplotypes shared between 2 samples. Analyzing with shared haplotypes is more robust than allele frequency analysis (for ex 23andMe uses haplotypes)

Blue indicates the highest number of shared haplotypes while yellow the lowest. As has been mentioned here Kurds and Iranians are almost indistinguishable genetically, that is why you see Kurds (Kurd F= Feyli Kurds, Kurd C=Kurmanji Kurds) sharing the maximum number of haplotypes (Blue) with Mazendarani Iranians, Zoroastrians, and Diploid Satsurbila. Iran N is underestimated because it is the haploid genome published by Lazaridis. I haven't had the time to process it for diploid genotypes yet. Once I do, its sharing will increase with some populations from Kurdistan to Pakistan.

The matrices also contain Caucasians, Europeans and ancient steppe samples that were imputed by Martiniano. The ones marked diploid, I processed and genotyped.

I have removed a large number of markers in linkage disequilibrium from the dataset


https://i.imgur.com/qeE0lty.png

https://i.imgur.com/bmCU1sK.png

Thanks, could you explain this for me?

Xehanort
10-09-2017, 07:05 PM
It ranges from 6-8%

Okay, makes sense. Did you have a great grandparent from Egypt?

Xehanort
10-09-2017, 07:06 PM
Of course not, I am from West Iran have around 80% adna continuity with Iran_CHL (used one of those Eurogenes K36 tools to determine), the rest is Anatolian farmer and some N. Euro admixture (that came in later with the Indo-Iranian migrations), so modern Iranians are obviously not the same as Ancient Iranians but they are close.

Yes, but Iran CHL is not accurate, a more accurate comparison would be to the Early Iron Age Iranian sample as that was following the Indo-European migrations. Let me know if you want the EIA kit number, I have it.

Zoran
10-09-2017, 07:25 PM
Yes, but Iran CHL is not accurate, a more accurate comparison would be to the Early Iron Age Iranian sample as that was following the Indo-European migrations. Let me know if you want the EIA kit number, I have it.

Alright, lets try again then:

Admix Results (sorted):

# Population Percent
1 West_Asia 45.62
2 SW_Europe 21.19
3 SW_Asia 15.51
4 NE_Europe 6.86
5 South_Asia 6.07
6 NE_Asia 1.6
7 East_Africa 0.93
8 Americas 0.93
9 Siberia 0.56
10 South_Africa 0.55
11 West_Africa 0.2

Iron Age Iran:

Admix Results (sorted):

# Population Percent
1 West_Asia 48.85
2 SW_Europe 23.02
3 SW_Asia 16.17
4 NE_Europe 10.71
5 South_Asia 1.25

Lupus82
10-09-2017, 07:29 PM
https://i.imgur.com/YGKrePe.png

Use this website for comparison and post a screenshot like I did, would be nice:



puntDNAL K13 Global...

1 West_Asia 43.99
2 SW_Europe 22.05
3 SW_Asia 14.68
4 NE_Europe 7.93
5 South_Asia 5.95
6 NE_Asia 1.83
7 Siberia 1.43
8 West_Africa 1.3
9 Americas 0.76
10 Oceania 0.08



What do these figures mean in the boxes in this picture?

19225

jesus
10-09-2017, 07:33 PM
Mostly east iranics such as, the Tajik Pamiris, yaghnobis, and pashtuns. They have 40-70% ancestry from them.

West iranics have 10-25%.

70% is way too high. Pamiris and yaghnobis score the highest pre BMAC steppe(around 45-55%). Pashtuns are pretty diverse and score anything from 28/25 to 40%.

Samples from Yaz and BMAC are needed in order to have a better picture. Also, early Persian/Median samples will be useful.

ancestryfan1994
10-09-2017, 09:32 PM
Okay, makes sense. Did you have a great grandparent from Egypt?

Yeah, in or around that timeframe it seems. There is a bunch of other stuff, but for the most part we are just regular Persian from the south of Iran.

Zoran
10-09-2017, 10:06 PM
puntDNAL K13 Global...

1 West_Asia 43.99
2 SW_Europe 22.05
3 SW_Asia 14.68
4 NE_Europe 7.93
5 South_Asia 5.95
6 NE_Asia 1.83
7 Siberia 1.43
8 West_Africa 1.3
9 Americas 0.76
10 Oceania 0.08



What do these figures mean in the boxes in this picture?

19225

The numbers represent the % of autosomal sharing you have with the samples, the more red the colour is the more similar.

Xehanort
10-10-2017, 12:12 AM
Alright, lets try again then:

Admix Results (sorted):

# Population Percent
1 West_Asia 45.62
2 SW_Europe 21.19
3 SW_Asia 15.51
4 NE_Europe 6.86
5 South_Asia 6.07
6 NE_Asia 1.6
7 East_Africa 0.93
8 Americas 0.93
9 Siberia 0.56
10 South_Africa 0.55
11 West_Africa 0.2

Iron Age Iran:

Admix Results (sorted):

# Population Percent
1 West_Asia 48.85
2 SW_Europe 23.02
3 SW_Asia 16.17
4 NE_Europe 10.71
5 South_Asia 1.25

Damn, almost the same. Just as I predicted. You seem to have 2% African ancestry, about 4% East Asian (Americas is basically East Asian) ancestry, and 7% South Asian ancestry, with a reduced European ancestry. So overall, I would say that you are 87% similar to Ancient Iranians, not bad. Where in Iran are you from? You seem to have a bit more African ancestry than most Iranians.

Xehanort
10-10-2017, 12:13 AM
Yeah, in or around that timeframe it seems. There is a bunch of other stuff, but for the most part we are just regular Persian from the south of Iran.

Okay, interesting. Yes, that Egyptian likely elevated your SSA admixture, unless your Egyptian ancestor was a Copt.

Xehanort
10-10-2017, 12:31 AM
70% is way too high. Pamiris and yaghnobis score the highest pre BMAC steppe(around 45-55%). Pashtuns are pretty diverse and score anything from 28/25 to 40%.

Samples from Yaz and BMAC are needed in order to have a better picture. Also, early Persian/Median samples will be useful.

It was probably 60 to 75% pre-Mongol invasion.

Zoran
10-10-2017, 01:40 AM
Damn, almost the same. Just as I predicted. You seem to have 2% African ancestry, about 4% East Asian (Americas is basically East Asian) ancestry, and 7% South Asian ancestry, with a reduced European ancestry. So overall, I would say that you are 87% similar to Ancient Iranians, not bad. Where in Iran are you from? You seem to have a bit more African ancestry than most Iranians.

My families originate around the Ilam Province, I might have a bit of Luri from my Paternal side, otherwise I'm mostly from Ilam.

Also 23andme didn't pick up any SSA, so it might just be noise.

Anyways I'll post some Feyli Kurds' results to compare:

Mine:

Admix Results (sorted):

# Population Percent
1 West_Asia 45.62
2 SW_Europe 21.19
3 SW_Asia 15.51
4 NE_Europe 6.86
5 South_Asia 6.07
6 NE_Asia 1.6
7 East_Africa 0.93
8 Americas 0.93
9 Siberia 0.56
10 South_Africa 0.55
11 West_Africa 0.2

Single Population Sharing:

# Population (source) Distance
1 Kurdish 3.33
2 Iranian 4.57
3 Azerbaijan_Azeri 6.08
4 Abkhasian 7.83
5 Armenian 10

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 76% Iranian + 24% Turkish_Trabzon @ 2.4
2 72.4% Iranian + 27.6% Armenian @ 2.72
3 98% Kurdish + 2% Japanese @ 2.84
4 98% Kurdish + 2% Korean @ 2.85
5 98% Kurdish + 2% Han_North_China @ 2.86

Feyli 1:

Admix Results (sorted):

# Population Percent
1 West_Asia 46.86
2 SW_Europe 18.26
3 SW_Asia 16.78
4 South_Asia 8.14
5 NE_Europe 6.71
6 Siberia 1.35
7 East_Africa 1.21
8 NE_Asia 0.43
9 Americas 0.26

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.02
2 Kurdish 4.81
3 Azerbaijan_Azeri 9.15
4 Abkhasian 10.53
5 Dagestan_Azeri 11.65

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 91.6% Iranian + 8.4% Assyrian @ 2.8
2 92.6% Iranian + 7.4% Armenian @ 2.86
3 96.6% Iranian + 3.4% Yemeni @ 2.89
4 94.6% Iranian + 5.4% Turkish_Trabzon @ 2.89
5 97.8% Iranian + 2.2% Saudi @ 2.92

Feyli 2:

Admix Results (sorted):

# Population Percent
1 West_Asia 46.09
2 SW_Europe 19.96
3 SW_Asia 15.84
4 South_Asia 8.67
5 NE_Europe 5.71
6 Siberia 1.42
7 Americas 0.93
8 SE_Asia 0.65
9 East_Africa 0.39
10 Oceania 0.23
11 South_Africa 0.11

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.74
2 Kurdish 4.68
3 Azerbaijan_Azeri 8.31
4 Abkhasian 10.1
5 Dagestan_Azeri 11.65

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 66.1% Armenian + 33.9% Makrani @ 2.39
2 64.8% Assyrian + 35.2% Brahui @ 2.45
3 64.7% Assyrian + 35.3% Balochi @ 2.5
4 65.5% Armenian + 34.5% Brahui @ 2.65
5 65.6% Assyrian + 34.4% Makrani @ 2.82

Feyli 3:

Admix Results (sorted):

# Population Percent
1 West_Asia 49.36
2 SW_Asia 18.1
3 SW_Europe 15.8
4 NE_Europe 6.11
5 South_Asia 5.65
6 SE_Asia 1.71
7 Siberia 1.52
8 South_Africa 1.41
9 East_Africa 0.29
10 Oceania 0.04
11 West_Africa 0.01

Single Population Sharing:

# Population (source) Distance
1 Iranian 6.63
2 Kurdish 7.51
3 Azerbaijan_Azeri 11.93
4 Abkhasian 12.42
5 Dagestan_Azeri 13.58

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 96.2% Iranian + 3.8% Bedouin @ 6.43
2 95.8% Iranian + 4.2% Saudi @ 6.45
3 95.1% Iranian + 4.9% Yemeni @ 6.5
4 90.9% Iranian + 9.1% Assyrian @ 6.51
5 93.2% Iranian + 6.8% Armenian @ 6.57

Feyli 4:

Admix Results (sorted):

# Population Percent
1 West_Asia 45.03
2 SW_Europe 20.1
3 SW_Asia 15.33
4 South_Asia 7.94
5 NE_Europe 7.16
6 Siberia 2.24
7 East_Africa 1.11
8 Americas 1
9 SE_Asia 0.08

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.38
2 Kurdish 3.99
3 Azerbaijan_Azeri 6.89
4 Abkhasian 9.04
5 Dagestan_Azeri 10.06


Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 86.4% Iranian + 13.6% Turkish_Trabzon @ 2.57
2 74.6% Iranian + 25.4% Azerbaijan_Azeri @ 2.6
3 65.6% Assyrian + 34.4% Pathan @ 2.69
4 66.5% Armenian + 33.5% Pathan @ 2.75
5 64.5% Assyrian + 35.5% Afghan_Pashtun @ 2.79

Feyli 5:

Admix Results (sorted):

# Population Percent
1 West_Asia 46.94
2 SW_Europe 17.69
3 SW_Asia 15.74
4 South_Asia 10.08
5 NE_Europe 5.64
6 Siberia 1.77
7 NE_Asia 0.62
8 East_Africa 0.61
9 South_Africa 0.49
10 Oceania 0.41

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.87
2 Kurdish 6.51
3 Azerbaijan_Azeri 10.3
4 Abkhasian 11.87
5 Dagestan_Azeri 12.47

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 58.4% Assyrian + 41.6% Brahui @ 3.21
2 59.1% Assyrian + 40.9% Makrani @ 3.25
3 59.5% Armenian + 40.5% Makrani @ 3.26
4 58.5% Assyrian + 41.5% Balochi @ 3.51
5 92.9% Iranian + 7.1% Brahui @ 3.57

Xehanort
10-10-2017, 02:19 AM
My families originate around the Ilam Province, I might have a bit of Luri from my Paternal side, otherwise I'm mostly from Ilam.

Also 23andme didn't pick up any SSA, so it might just be noise.

Anyways I'll post some Feyli Kurds' results to compare:

Mine:

Admix Results (sorted):

# Population Percent
1 West_Asia 45.62
2 SW_Europe 21.19
3 SW_Asia 15.51
4 NE_Europe 6.86
5 South_Asia 6.07
6 NE_Asia 1.6
7 East_Africa 0.93
8 Americas 0.93
9 Siberia 0.56
10 South_Africa 0.55
11 West_Africa 0.2

Single Population Sharing:

# Population (source) Distance
1 Kurdish 3.33
2 Iranian 4.57
3 Azerbaijan_Azeri 6.08
4 Abkhasian 7.83
5 Armenian 10

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 76% Iranian + 24% Turkish_Trabzon @ 2.4
2 72.4% Iranian + 27.6% Armenian @ 2.72
3 98% Kurdish + 2% Japanese @ 2.84
4 98% Kurdish + 2% Korean @ 2.85
5 98% Kurdish + 2% Han_North_China @ 2.86

Feyli 1:

Admix Results (sorted):

# Population Percent
1 West_Asia 46.86
2 SW_Europe 18.26
3 SW_Asia 16.78
4 South_Asia 8.14
5 NE_Europe 6.71
6 Siberia 1.35
7 East_Africa 1.21
8 NE_Asia 0.43
9 Americas 0.26

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.02
2 Kurdish 4.81
3 Azerbaijan_Azeri 9.15
4 Abkhasian 10.53
5 Dagestan_Azeri 11.65

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 91.6% Iranian + 8.4% Assyrian @ 2.8
2 92.6% Iranian + 7.4% Armenian @ 2.86
3 96.6% Iranian + 3.4% Yemeni @ 2.89
4 94.6% Iranian + 5.4% Turkish_Trabzon @ 2.89
5 97.8% Iranian + 2.2% Saudi @ 2.92

Feyli 2:

Admix Results (sorted):

# Population Percent
1 West_Asia 46.09
2 SW_Europe 19.96
3 SW_Asia 15.84
4 South_Asia 8.67
5 NE_Europe 5.71
6 Siberia 1.42
7 Americas 0.93
8 SE_Asia 0.65
9 East_Africa 0.39
10 Oceania 0.23
11 South_Africa 0.11

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.74
2 Kurdish 4.68
3 Azerbaijan_Azeri 8.31
4 Abkhasian 10.1
5 Dagestan_Azeri 11.65

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 66.1% Armenian + 33.9% Makrani @ 2.39
2 64.8% Assyrian + 35.2% Brahui @ 2.45
3 64.7% Assyrian + 35.3% Balochi @ 2.5
4 65.5% Armenian + 34.5% Brahui @ 2.65
5 65.6% Assyrian + 34.4% Makrani @ 2.82

Feyli 3:

Admix Results (sorted):

# Population Percent
1 West_Asia 49.36
2 SW_Asia 18.1
3 SW_Europe 15.8
4 NE_Europe 6.11
5 South_Asia 5.65
6 SE_Asia 1.71
7 Siberia 1.52
8 South_Africa 1.41
9 East_Africa 0.29
10 Oceania 0.04
11 West_Africa 0.01

Single Population Sharing:

# Population (source) Distance
1 Iranian 6.63
2 Kurdish 7.51
3 Azerbaijan_Azeri 11.93
4 Abkhasian 12.42
5 Dagestan_Azeri 13.58

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 96.2% Iranian + 3.8% Bedouin @ 6.43
2 95.8% Iranian + 4.2% Saudi @ 6.45
3 95.1% Iranian + 4.9% Yemeni @ 6.5
4 90.9% Iranian + 9.1% Assyrian @ 6.51
5 93.2% Iranian + 6.8% Armenian @ 6.57

Feyli 4:

Admix Results (sorted):

# Population Percent
1 West_Asia 45.03
2 SW_Europe 20.1
3 SW_Asia 15.33
4 South_Asia 7.94
5 NE_Europe 7.16
6 Siberia 2.24
7 East_Africa 1.11
8 Americas 1
9 SE_Asia 0.08

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.38
2 Kurdish 3.99
3 Azerbaijan_Azeri 6.89
4 Abkhasian 9.04
5 Dagestan_Azeri 10.06


Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 86.4% Iranian + 13.6% Turkish_Trabzon @ 2.57
2 74.6% Iranian + 25.4% Azerbaijan_Azeri @ 2.6
3 65.6% Assyrian + 34.4% Pathan @ 2.69
4 66.5% Armenian + 33.5% Pathan @ 2.75
5 64.5% Assyrian + 35.5% Afghan_Pashtun @ 2.79

Feyli 5:

Admix Results (sorted):

# Population Percent
1 West_Asia 46.94
2 SW_Europe 17.69
3 SW_Asia 15.74
4 South_Asia 10.08
5 NE_Europe 5.64
6 Siberia 1.77
7 NE_Asia 0.62
8 East_Africa 0.61
9 South_Africa 0.49
10 Oceania 0.41

Single Population Sharing:

# Population (source) Distance
1 Iranian 3.87
2 Kurdish 6.51
3 Azerbaijan_Azeri 10.3
4 Abkhasian 11.87
5 Dagestan_Azeri 12.47

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 58.4% Assyrian + 41.6% Brahui @ 3.21
2 59.1% Assyrian + 40.9% Makrani @ 3.25
3 59.5% Armenian + 40.5% Makrani @ 3.26
4 58.5% Assyrian + 41.5% Balochi @ 3.51
5 92.9% Iranian + 7.1% Brahui @ 3.57

I agree with you, I think that's certainly what's going on here. Undoubtedly. However, I was wondering. What do you think accounts for the elevated South Asian admixture in contemporary Iranians? Also, there's an Iran_Recent sample to compare with as well. It's from a Kurdish woman from the 15th century, and comparisons would be quite interesting. Let me know if you can't find the kit, and I'll look it up in my database. I think it's very similar to the Ancient Iranian sample, as there's no African or East Asian present, and just a bit more South Asian. Could it be Gypsy ancestry? I heard that Gypsies had a presence in Iran in the past.

MonkeyDLuffy
10-10-2017, 02:24 AM
I agree with you, I think that's certainly what's going on here. Undoubtedly. However, I was wondering. What do you think accounts for the elevated South Asian admixture in contemporary Iranians? Also, there's an Iran_Recent sample to compare with as well. It's from a Kurdish woman from the 15th century, and comparisons would be quite interesting. Let me know if you can't find the kit, and I'll look it up in my database. I think it's very similar to the Ancient Iranian sample, as there's no African or East Asian present, and just a bit more South Asian. Could it be Gypsy ancestry? I heard that Gypsies had a presence in Iran in the past.

They are neighboring populations, they share same genetic components except the ASI which is very minor (2-5% in most cases) in eastern Iran and gets higher when you move east.

Zoran
10-10-2017, 02:25 AM
I agree with you, I think that's certainly what's going on here. Undoubtedly. However, I was wondering. What do you think accounts for the elevated South Asian admixture in contemporary Iranians? Also, there's an Iran_Recent sample to compare with as well. It's from a Kurdish woman from the 15th century, and comparisons would be quite interesting. Let me know if you can't find the kit, and I'll look it up in my database. I think it's very similar to the Ancient Iranian sample, as there's no African or East Asian present, and just a bit more South Asian. Could it be Gypsy ancestry? I heard that Gypsies had a presence in Iran in the past.

I doubt Gypsies had any significant effect on the overall Iranian population since the South Asian component in Iran is ancient, it has decreased by time since Iran_Neolithic, its slightly higher in the South and I think it has to due with Australoid admixture increasing the further South and East you go, anyways here is her results:

Admix Results (sorted):

# Population Percent
1 West_Asia 48.58
2 SW_Europe 20.39
3 SW_Asia 16.12
4 NE_Europe 8.94
5 South_Asia 4.91
6 Siberia 0.89
7 Americas 0.18

Single Population Sharing:

# Population (source) Distance
1 Kurdish 2.88
2 Iranian 5.07
3 Abkhasian 6.97
4 Azerbaijan_Azeri 7.88
5 Dagestan_Azeri 9.71


Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 98.4% Kurdish + 1.6% Abkhasian @ 2.88
2 100% Kurdish + 0% Adygei @ 2.88
3 100% Kurdish + 0% Afghan_Hazara @ 2.88
4 100% Kurdish + 0% Afghan_Pashtun @ 2.88
5 100% Kurdish + 0% Afghan_Uzbeki @ 2.88

Sample is from Kermanshah and is only slightly more Northern shifted in comparison to me.

This is Iran_Mesolithic from the Mazandaran region in Northern Iran, the oldest sample from Iran and it also has South Asian admixture:

Admix Results (sorted):

# Population Percent
1 West_Asia 67.62
2 NE_Europe 13.16
3 SW_Europe 7.53
4 West_Africa 6.14
5 South_Asia 5.55

Single Population Sharing:

# Population (source) Distance
1 Dagestan_Azeri 27.04
2 Makrani 27.99
3 Balochi 28.02
4 Brahui 28.22
5 Abkhasian 28.24

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 51.7% Makrani + 48.3% Adygei @ 24.12
2 51.5% Makrani + 48.5% Chechen @ 24.13
3 50.8% Makrani + 49.2% Abkhasian @ 24.14
4 50.8% Brahui + 49.2% Chechen @ 24.28
5 53.9% Dagestan_Azeri + 46.1% Makrani @ 24.29

Xehanort
10-10-2017, 03:16 AM
I doubt Gypsies had any significant effect on the overall Iranian population since the South Asian component in Iran is ancient, it has decreased by time since Iran_Neolithic, its slightly higher in the South and I think it has to due with Australoid admixture increasing the further South and East you go, anyways here is her results:

Admix Results (sorted):

# Population Percent
1 West_Asia 48.58
2 SW_Europe 20.39
3 SW_Asia 16.12
4 NE_Europe 8.94
5 South_Asia 4.91
6 Siberia 0.89
7 Americas 0.18

Single Population Sharing:

# Population (source) Distance
1 Kurdish 2.88
2 Iranian 5.07
3 Abkhasian 6.97
4 Azerbaijan_Azeri 7.88
5 Dagestan_Azeri 9.71


Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 98.4% Kurdish + 1.6% Abkhasian @ 2.88
2 100% Kurdish + 0% Adygei @ 2.88
3 100% Kurdish + 0% Afghan_Hazara @ 2.88
4 100% Kurdish + 0% Afghan_Pashtun @ 2.88
5 100% Kurdish + 0% Afghan_Uzbeki @ 2.88

Sample is from Kermanshah and is only slightly more Northern shifted in comparison to me.

This is Iran_Mesolithic from the Mazandaran region in Northern Iran, the oldest sample from Iran and it also has South Asian admixture:

Admix Results (sorted):

# Population Percent
1 West_Asia 67.62
2 NE_Europe 13.16
3 SW_Europe 7.53
4 West_Africa 6.14
5 South_Asia 5.55

Single Population Sharing:

# Population (source) Distance
1 Dagestan_Azeri 27.04
2 Makrani 27.99
3 Balochi 28.02
4 Brahui 28.22
5 Abkhasian 28.24

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 51.7% Makrani + 48.3% Adygei @ 24.12
2 51.5% Makrani + 48.5% Chechen @ 24.13
3 50.8% Makrani + 49.2% Abkhasian @ 24.14
4 50.8% Brahui + 49.2% Chechen @ 24.28
5 53.9% Dagestan_Azeri + 46.1% Makrani @ 24.29

Alright, thanks. You're right about much of what you have said, and thanks for making the comparisons. However, I observed that the South Asian admixture decreased in Iran following the arrival of the Indo-Europeans (EIA), and then increased following the Islamic conquest, what do you think accounts for this? Could it be Baloch movement west? Since Balochis have significant South Asian (excluding ASI which is only 10 to 14% in them) ancestry. Also, could you explain the distance function to me? Say if the distance is 5.88, does that mean that the person in question is about 94.12% similar to the closest population? Thanks!

Xehanort
10-10-2017, 03:17 AM
They are neighboring populations, they share same genetic components except the ASI which is very minor (2-5% in most cases) in eastern Iran and gets higher when you move east.

Okay, makes sense.

Zoran
10-10-2017, 03:19 AM
Alright, thanks. You're right about much of what you have said, and thanks for making the comparisons. However, I observed that the South Asian admixture decreased in Iran following the arrival of the Indo-Europeans (EIA), and then increased following the Islamic conquest, what do you think accounts for this? Could it be Baloch movement west? Since Balochis have significant South Asian (excluding ASI which is only 10 to 14% in them) ancestry. Also, could you explain the distance function to me? Say if the distance is 5.88, does that mean that the person in question is about 94.12% similar to the closest population? Thanks!

Not quite, South Asian has basically been on the decrease since Neolithic times, SW Asian and Anatolian Farmer admixture started to increase as well which is why the South Asian admixture decreased. The reason why South Asian has increased some places is because of internal population movements, people have mixed with each other after Iran became unified where as Pre-Iranic Iran was split and dominated by various pre-Iranic kingdoms that explains their genetical differences. The Islamic conquest of Iran has only had very little effect and those are specified to the most Southern part of the country.

Distance is how close you are to given population, the smaller the number is the closer you are to the population basically.

ancestryfan1994
10-10-2017, 03:24 AM
I agree with you, I think that's certainly what's going on here. Undoubtedly. However, I was wondering. What do you think accounts for the elevated South Asian admixture in contemporary Iranians? Also, there's an Iran_Recent sample to compare with as well. It's from a Kurdish woman from the 15th century, and comparisons would be quite interesting. Let me know if you can't find the kit, and I'll look it up in my database. I think it's very similar to the Ancient Iranian sample, as there's no African or East Asian present, and just a bit more South Asian. Could it be Gypsy ancestry? I heard that Gypsies had a presence in Iran in the past.

Even though Gypsies do have a very minor presence in Iran, they definitely didn't impact the population, I can only think of possible Baluch ancestry in Iranians with a very elevated south asian score, but its hard to tell to be honest, and I don't know what the genetic profile of the Iranian Baluch is like. There has also been movement between Iran and India in recent times, many Indians worked in Iran during the last couple of centuries, and obviously there may have also been back migration from the Parsi, but no real statistics show how many of them were around. My father actually went to school with two Sikhs back in the 50-60s

khanabadoshi
10-10-2017, 04:44 AM
Even though Gypsies do have a very minor presence in Iran, they definitely didn't impact the population, I can only think of possible Baluch ancestry in Iranians with a very elevated south asian score, but its hard to tell to be honest, and I don't know what the genetic profile of the Iranian Baluch is like. There has also been movement between Iran and India in recent times, many Indians worked in Iran during the last couple of centuries, and obviously there may have also been back migration from the Parsi, but no real statistics show how many of them were around. My father actually went to school with two Sikhs back in the 50-60s

They tend to have lower ASI than the Pakistani Baloch/Makrani or Emerati Baluch and sometimes other Iranians/Tajiks. However, it depends on how ASI/SI/Indian is defined in a particular calculator, so I can't draw conclusions. The three Iranian Baluch samples we post are related to each other [cousins/uncle] and one of them is maternally mixed with Persian Jewish or something from the Gulf (it has slipped my mind), so we probably aren't getting a representative scope of the variation possible in Sistan-o Baluchestan. I'll post some Iranian, Omani/Emerati, and Pakistani Baloch scores if you like. Which calculator are you guys comparing on?

Xehanort
10-10-2017, 04:47 AM
Even though Gypsies do have a very minor presence in Iran, they definitely didn't impact the population, I can only think of possible Baluch ancestry in Iranians with a very elevated south asian score, but its hard to tell to be honest, and I don't know what the genetic profile of the Iranian Baluch is like. There has also been movement between Iran and India in recent times, many Indians worked in Iran during the last couple of centuries, and obviously there may have also been back migration from the Parsi, but no real statistics show how many of them were around. My father actually went to school with two Sikhs back in the 50-60s

Yes, but the recent migrants to India didn't really mix. I remember reading that there were a lot of Indians in the Safavid Empire, even around 20,000 in Isfahan alone during the city's height. Perhaps that could explain it as well.

Xehanort
10-10-2017, 04:47 AM
They tend to have lower ASI than the Pakistani Baloch/Makrani or Emerati Baluch and sometimes other Iranians/Tajiks. However, it depends on how ASI/SI/Indian is defined in a particular calculator, so I can't draw conclusions. The three Iranian Baluch samples we post are related to each other [cousins/uncle], so we probably aren't getting a representative scope of the variation possible in Sistan-o Baluchestan. I'll post some Iranian, Omani/Emerati, and Pakistani Baloch scores if you like. Which calculator are you guys comparing on?

Can I see the results of the Iranian Baloch, thanks.

Xehanort
10-10-2017, 04:49 AM
Not quite, South Asian has basically been on the decrease since Neolithic times, SW Asian and Anatolian Farmer admixture started to increase as well which is why the South Asian admixture decreased. The reason why South Asian has increased some places is because of internal population movements, people have mixed with each other after Iran became unified where as Pre-Iranic Iran was split and dominated by various pre-Iranic kingdoms that explains their genetical differences. The Islamic conquest of Iran has only had very little effect and those are specified to the most Southern part of the country.

Distance is how close you are to given population, the smaller the number is the closer you are to the population basically.

Also, Zoran. I was wondering, how close is 8.9, if it says that you are @8.9 close to a certain population, does that essentially mean that 91.1% of your DNA is shared with that population?

khanabadoshi
10-10-2017, 04:50 AM
Can I see the results of the Iranian Baloch, thanks.

On which calculator? puntK13?

Xehanort
10-10-2017, 05:15 AM
On which calculator? puntK13?

Yeah, is that the most accurate for Iranians/South Asians after Harappa? Could you do Harappa and puntK13? Thanks

khanabadoshi
10-10-2017, 05:21 AM
Yes, but the recent migrants to India didn't really mix. I remember reading that there were a lot of Indians in the Safavid Empire, even around 20,000 in Isfahan alone during the city's height. Perhaps that could explain it as well.

ASI is a theoretical component, so it is possible that percentage seen in Iran on varying calculators is actually just alleles getting assigned to ASI instead of Iran N (this is because Iran N is haploid and underestimated in most calculators per Kurd's observations). My hypothesis is that the ASI will disappear for most Iranians with diploid Iran N in the picture. The 4-10% seen in non-Baluch-Iranians will go down to 0-2%. This in turn is probably means that the Baloch and S/SC Asians are inflated by similar proportions, so their Iran N should increase and ASI decrease. Basically, I think it's a reasonable possibility that if a person in Western Iran is scoring 6-9% ASI -- it's likely Iran N -- and ASI is being overestimated while Iran N is underestimated by 5-8% overall from Kurdistan to Bangladesh. Of course all this depends on how one defines ASI -- let's hope aDNA in the coming months allows "ASI" to define itself!

khanabadoshi
10-10-2017, 05:30 AM
POPULATION

West_Asia
NE_Europe
Americas
Siberia
Oceania
South_Asia
NE_Asia
East_Africa
SE_Asia
SW_Europe
SW_Asia
West_Africa
South_Africa


BALOCH 01
61.16

8.66
0.78
1.71
0.31
19.92

0
2.35
0
0.32
4.8

0
0


BALOCH 02
57.14
12.21
0.32
0.63
0.52
20.67
0
0.12
0
0.91
6.7
0.51
0.27


BALOCH 03 [Outlier]
48.45

7.99
1.4
0.23

1.27
30.66

1.74
1.52
0.37
1.84
4.53
0
0


BALOCH 04 [W African Outlier]
44.02

7.17

1.8
0
0
16.64

0
3.88
1.37
3.53
7.89

12.35

1.36


BALOCH 05
52.98

9.87
1.07

1.39

0.85
26.74
0

1.12
0
1.01

4.34
0.62
0


BALOCH 06 [W African Outlier]
49.81

6.09
1.13
0
1.52
19.06
0
3.5
0
2.36
6.8
8.8

0.9


BALOCH 07
59.19

7.35
1.27

0

0
18.55
0
0
0.94
1.51
8.58
1.98
0.63


BALOCH 08
57.63
10.31

1.36
0
0.14
21.08
0.63
0.81
0
2.84
3.33
0.18
1.7


BALOCH 09 [East Asian Outlier]
53.67

8.66
1.3

4.21

0.99
18.18
1.02

1.08
2.29

2.92
4.88

0
0.81


BALOCH 10 [Extreme Outlier]
34.3

9
1.12

2.26
0.84
48.32

0.09
0.84
2.05
0
1.09
0.05
0


BALOCH 11
54.73

11.76
1.28

0
0.47
24.03

0.19

3.06
0
0
4.48
0
0


BALOCH 12
58.81
7.66
0.51
1.57
0.14
20.1
0
0.93
0.62
0.23
7.87
1.57
0


BALOCH 13 [W African Outlier]
52.33

6.32
0.56
0
0.56
18.2
0.78

2.22
0
1.5

8.73

7.99

0.8


BALOCH 14
54.16
9.69
0.65
1.03
0
18.07

0
3.83
0.24
3.82
5.77

2.74
0


BALOCH 15
58.02
7.54
0.5
0.51
0
20.92
0.49
1.31
0
0.64
7.79
2.26
0


BALOCH 16
55.95
11.43
1.32
0.66
0.5
22.19
0.78
0.86
0
3.39
2.19

0
0.7


BALOCH 17
52.22
12.33
2.15
0.18
1.13
22.8
0.26
0.75
0
4.96
2.19
0.57
0.44


BALOCH 18
62.41
7.93
1.03
0.28
0
20.49
0
0.95
0.72
1.71
3.21
0.86
0.41


BALOCH 19
57.74

7.89
1.29
0.49
0
20.12
0
1.83
1.05
4.31
4.64
0
0.65


BALOCH 20
53.14
8.77
0
1.56
0
28.41
0
2.2
0
2.03
1.54
2.36
0


BALOCH 21
54.32
6.39
0.7
0.06
0.81
28.71
0
1.91
0.59
0
6.5
0
0


BALOCH 22
52.35
11.44
1.1
0
0.55
26.75
0
1.11
1.02
0
4.21
1.47
0


BALOCH 23
55.48
8.87
0
0
0.19
25.03
0
0.18
1.85
0
4.8
3.22
0.38


BALOCH 24

53.49

9.73
0
0
0.96
24.47
1.76
1.5
0
0
4.51
3.51
0


BALOCH AVERAGE

53.89583

8.960833

0.94333
0.699
0.4896
23.33792
0.3225

1.5775
0.546
1.659583
5.0571
2.1266667

0.3770833


















BALUCH IRAN 1
48.44

10.15
0
1.8
0.63
15.66

0
1.2
0
5.52
13.47

2.8
0.33


BALUCH IRAN 2
46.29
10.51
0
1.67
0.06
18.67
0
1.34
0.58
5.02
11.58
3.25
1.02


BALUCH IRAN 3

48.26

9.51
0.44
1.05

0.65
16.15
0

1
0.32
6.05
13.21
2.53
0.82


BALUCH IRAN AVERAGE

47.66333

10.05667

0.14667
1.507
0.4467
16.82667
0

1.18
0.3
5.53
12.753
2.86

0.7233333


















BALUCH EMIRATI 01
53.72

6.6
1
1.23
0.33
16.74

0
0.11

0.27
6.04
7.48

6.14
0.34


BALUCH EMIRATI 02
50.24
7.89
2.24
1.64
0.08
20.13
0
0
0.4
5.48
9.61
1.8
0.49


BALUCH EMIRATI 03

49.58

7.11
0
0.68
0
18.01
0
0
1.27
10.03
9.96
3.19
0.15


BALUCH EMIRATI AVERAGE

51.18

7.2

1.08
1.183
0.1367
18.29333
0

0.036667
0.647
7.183333
9.0167
3.71

0.3266667



Basically Pakistani Baloch are scoring more W Asian/S Asian and less SW Asian; while Iranian Baluch are scoring less W Asian/S Asian and more SW Asian -- but keep in mind that the Iranian Baluch are all related, so this maybe because they are in fact all mixed with something more recently from SW Asia. It is interesting that they are scoring more SW Asian than the Emirati Baloch, who seem to be in between the Pakistani Baloch and Iranian Baluch in general (with slightly more W/S Asian and slightly less SW Asian overall as compared to the Iranian Baluch).

Xehanort
10-10-2017, 05:40 AM
ASI is a theoretical component, so it is possible that percentage seen in Iran on varying calculators is actually just alleles getting assigned to ASI instead of Iran N (this is because Iran N is haploid and underestimated in most calculators per Kurd's observations). My hypothesis is that the ASI will disappear for most Iranians with diploid Iran N in the picture. The 4-10% seen in non-Baluch-Iranians will go down to 0-2%. This in turn is probably means that the Baloch and S/SC Asians are inflated by similar proportions, so their Iran N should increase and ASI decrease. Basically, I think it's a reasonable possibility that if a person in Western Iran is scoring 6-9% ASI -- it's likely Iran N -- and ASI is being overestimated while Iran N is underestimated by 5-8% overall from Kurdistan to Bangladesh. Of course all this depends on how one defines ASI -- let's hope aDNA in the coming months allows "ASI" to define itself!

Yes, I have read about the Rakhigarhi study. That should be interesting. Personally, I think that the founders of the Indus Valley Civilization were around 50% Neolithic Iranian, and 50% some sort of Veddoid-Caucasoid hybrid. Also, thanks for the Baloch samples, appreciate it. I also like your explanation. I think it is possible that ASI is heavily influenced by Iran Neolithic.

Xehanort
10-10-2017, 06:22 AM
Bro, can you also post the K13 results for Iranian Zoroastrians, if you have them? Thanks!

khanabadoshi
10-10-2017, 07:05 AM
Bro, can you also post the K13 results for Iranian Zoroastrians, if you have them? Thanks!

I haven't extracted them yet. I will post them when I do.

Lupus82
10-10-2017, 07:07 AM
Would you also post the Near East Neolithic K13 for Iranians?

Here is mine:

1 IRAN_NEOLITHIC 30.29
2 CHG_EEF 24.56
3 NATUFIAN 14.49
4 ANATOLIA_NEOLITHIC 12.34
5 ANCESTRAL_INDIAN 8.71
6 EHG 6.61
7 POLAR 2.75


Also, I have gotten tested both by AncestryDNA and 23andme Which one of these corporations provide the most accurate results? Any ideas?

khanabadoshi
10-10-2017, 07:17 AM
Would you also post the Near East Neolithic K13 for Iranians?

Here is mine:

1 IRAN_NEOLITHIC 30.29
2 CHG_EEF 24.56
3 NATUFIAN 14.49
4 ANATOLIA_NEOLITHIC 12.34
5 ANCESTRAL_INDIAN 8.71
6 EHG 6.61
7 POLAR 2.75


Also, I have gotten tested both by AncestryDNA and 23andme Which one of these corporations provide the most accurate results? Any ideas?

Will do. As far as Gedmatch Calculators are concerned, 23andme almost always has more overlap with the genomes used to form components on most of the calculators. So, when posting results for autosomal comparison, your best bet is to use 23andme > FTDNA/Genographic > AncestryDNA > LivingDNA/Genecove.

When it comes to plotting, if a person posts both 23andme results and FTDNA results, I usually only plot their 23andme results. If they post FTDNA and AncestryDNA, I usually only plot their FTDNA. I tend to only plot AncestryDNA, LivingDNA, or FTDNA if that is the only option available for the person. I usually post all of my own results on each plot (23andme/FTDNA/LivingDNA) to illustrate the difference between the results. Sometimes FTDNA/AncestryDNA and 23andme are very close on a calculator and it doesn't matter which result someone posts. LivingDNA is usually significantly different in any scenario; so-much-so, that I am considering never plotting LivingDNA results against any of the other companies, because it is misleading. I'm of the opinion that LivingDNA results can only be compared to other LivingDNA results.

If I was going for maximum accuracy, I would make separate spreadsheets/plots for each company. However, that would be pretty time-consuming.

EDIT: You can see the SNP overlap difference between my 23andme, FTDNA, and LivingDNA results against the HGDP samples here (439K vs. 363K vs. 112K):

https://i.gyazo.com/fe714d847494b1eedc0d7181dbd2bb0d.png

Xehanort
10-10-2017, 02:59 PM
I haven't extracted them yet. I will post them when I do.

Why is LivingDNA worse than all others? I thought that it was much better since it had a better breakdown? And thanks! :)

Zoran
10-10-2017, 04:12 PM
Would you also post the Near East Neolithic K13 for Iranians?

Here is mine:

1 IRAN_NEOLITHIC 30.29
2 CHG_EEF 24.56
3 NATUFIAN 14.49
4 ANATOLIA_NEOLITHIC 12.34
5 ANCESTRAL_INDIAN 8.71
6 EHG 6.61
7 POLAR 2.75


Also, I have gotten tested both by AncestryDNA and 23andme Which one of these corporations provide the most accurate results? Any ideas?

Admix Results (sorted):

# Population Percent
1 IRAN_NEOLITHIC 36.11
2 CHG_EEF 22.86
3 NATUFIAN 14.38
4 ANATOLIA_NEOLITHIC 12.51
5 ANCESTRAL_INDIAN 5.54
6 EHG 4.81
7 SIBERIAN 1.79
8 PAPUAN 1.26
9 SUB_SAHARAN 0.74

Lupus82
10-10-2017, 09:39 PM
Admix Results (sorted):


1

It looks like I am quite Iranian in spite of living in Anatolia.

khanabadoshi
10-10-2017, 10:15 PM
Why is LivingDNA worse than all others? I thought that it was much better since it had a better breakdown? And thanks! :)

It's not necessarily worse, it's just the SNPs it tests for often don't overlap well with others. In the NearEast Neolithic K13 23andme, FTDNA, and LivingDNA are pretty similar.



NEAR EAST NEOLITHIC K13
SE_ASIAN
ANATOLIA_NEOLITHIC
CHG_EEF
POLAR
EHG
SUB_SAHARAN
IRAN_NEOLITHIC
KARITIANA
ANCESTRAL_INDIAN
NATUFIAN
SIBERIAN
PAPUAN
SHG_WHG


khanabadoshi 23andme
0.00%
0.44%
5.51%
0.00%
12.42%
0.07%
38.45%
1.51%
39.53%
1.67%
0.40%
0.00%
0.00%


khana FTDNA
0.00%
1.89%
4.68%
0.00%
11.84%
0.00%
37.83%
1.71%
39.59%
1.73%
0.72%
0.00%
0.01%


khana LivingDNA
0.00%
0.34%
4.43%
0.00%
13.40%
0.00%
36.72%
2.12%
39.66%
1.10%
2.23%
0.00%
0.00%

khanabadoshi
10-10-2017, 10:19 PM
Here are some Baloch/Pashtun scores; I added my uncle as well for comparison. I'll run the Iranians and Tajiks sometime this week.



NEAR EAST NEOLITHIC K13
SE_ASIAN
ANATOLIA_NEOLITHIC
CHG_EEF
POLAR
EHG
SUB_SAHARAN
IRAN_NEOLITHIC
KARITIANA
ANCESTRAL_INDIAN
NATUFIAN
SIBERIAN
PAPUAN
SHG_WHG


AFG - Pashtun [Achakzai]
5.51%
0.00%
13.99%
0.53%
11.22%
0.00%
34.33%
2.19%
22.24%
3.83%
2.37%
0.00%
3.79%


AFG - Pashtun [Barak]
1.59%
1.37%
17.78%
0.10%
10.69%
0.27%
35.82%
1.17%
18.96%
5.39%
3.73%
1.01%
2.13%


AFG - Pashtun [Barakzai]
3.62%
1.30%
16.22%
0.62%
11.94%
0.00%
34.13%
2.01%
22.64%
4.54%
0.00%
0.00%
2.97%


AFG - Pashtun [Mohammadzai]
1.88%
4.39%
17.94%
0.00%
8.87%
0.13%
35.08%
0.41%
18.77%
8.14%
2.50%
0.00%
1.90%


Mohmand - Pashtun
0.00%
2.72%
18.48%
0.00%
12.47%
0.65%
35.86%
1.86%
23.45%
0.10%
2.49%
0.76%
1.17%


PATHAN_HGDP00213
0.00%
0.24%
17.84%
0.43%
9.85%
0.00%
39.10%
0.00%
26.61%
0.96%
0.00%
0.98%
3.99%


PATHAN_HGDP00214
1.56%
1.71%
18.72%
0.00%
9.26%
0.08%
36.81%
0.46%
18.39%
6.20%
3.08%
0.39%
3.35%


BALOCH_HGDP0052
0.00%
1.86%
7.64%
0.00%
7.14%
0.00%
52.40%
0.79%
24.76%
3.89%
0.00%
0.00%
1.51%


BALOCH_HGDP0054
0.00%
5.61%
8.62%
0.54%
9.86%
0.00%
48.50%
0.00%
20.97%
4.74%
0.00%
0.00%
1.15%


BRAHUI_HGDP00001
0.00%
0.28%
6.18%
0.00%
6.20%
0.39%
50.11%
0.00%
25.90%
6.91%
0.00%
0.00%
4.04%


BRAHUI_HGDP00003
0.00%
9.50%
2.48%
1.78%
4.90%
0.79%
54.69%
0.00%
24.21%
1.21%
0.00%
0.44%
0.00%


pUncle - jam [Baloch/Kashmiri]
0.00%
0.65%
7.25%
0.00%
11.52%
0.81%
41.50%
0.38%
37.46%
0.33%
0.00%
0.09%
0.01%

Xehanort
10-11-2017, 06:39 AM
Here are some Baloch/Pashtun scores; I added my uncle as well for comparison. I'll run the Iranians and Tajiks sometime this week.



NEAR EAST NEOLITHIC K13
SE_ASIAN
ANATOLIA_NEOLITHIC
CHG_EEF
POLAR
EHG
SUB_SAHARAN
IRAN_NEOLITHIC
KARITIANA
ANCESTRAL_INDIAN
NATUFIAN
SIBERIAN
PAPUAN
SHG_WHG


AFG - Pashtun [Achakzai]
5.51%
0.00%
13.99%
0.53%
11.22%
0.00%
34.33%
2.19%
22.24%
3.83%
2.37%
0.00%
3.79%


AFG - Pashtun [Barak]
1.59%
1.37%
17.78%
0.10%
10.69%
0.27%
35.82%
1.17%
18.96%
5.39%
3.73%
1.01%
2.13%


AFG - Pashtun [Barakzai]
3.62%
1.30%
16.22%
0.62%
11.94%
0.00%
34.13%
2.01%
22.64%
4.54%
0.00%
0.00%
2.97%


AFG - Pashtun [Mohammadzai]
1.88%
4.39%
17.94%
0.00%
8.87%
0.13%
35.08%
0.41%
18.77%
8.14%
2.50%
0.00%
1.90%


Mohmand - Pashtun
0.00%
2.72%
18.48%
0.00%
12.47%
0.65%
35.86%
1.86%
23.45%
0.10%
2.49%
0.76%
1.17%


PATHAN_HGDP00213
0.00%
0.24%
17.84%
0.43%
9.85%
0.00%
39.10%
0.00%
26.61%
0.96%
0.00%
0.98%
3.99%


PATHAN_HGDP00214
1.56%
1.71%
18.72%
0.00%
9.26%
0.08%
36.81%
0.46%
18.39%
6.20%
3.08%
0.39%
3.35%


BALOCH_HGDP0052
0.00%
1.86%
7.64%
0.00%
7.14%
0.00%
52.40%
0.79%
24.76%
3.89%
0.00%
0.00%
1.51%


BALOCH_HGDP0054
0.00%
5.61%
8.62%
0.54%
9.86%
0.00%
48.50%
0.00%
20.97%
4.74%
0.00%
0.00%
1.15%


BRAHUI_HGDP00001
0.00%
0.28%
6.18%
0.00%
6.20%
0.39%
50.11%
0.00%
25.90%
6.91%
0.00%
0.00%
4.04%


BRAHUI_HGDP00003
0.00%
9.50%
2.48%
1.78%
4.90%
0.79%
54.69%
0.00%
24.21%
1.21%
0.00%
0.44%
0.00%


pUncle - jam [Baloch/Kashmiri]
0.00%
0.65%
7.25%
0.00%
11.52%
0.81%
41.50%
0.38%
37.46%
0.33%
0.00%
0.09%
0.01%



Thanks, is this PuntDNAL? Or is it Gedrosia? Because I cannot find the Neolthic K13 Near East calculator on Gedmatch. It's simply not there. Your Ancestral Indian is way off for a Pathan (I remember telling me that you are a Pathan and Tajik). It's weird, very, very weird.

khanabadoshi
10-11-2017, 07:29 AM
Thanks, is this PuntDNAL? Or is it Gedrosia? Because I cannot find the Neolthic K13 Near East calculator on Gedmatch. It's simply not there. Your Ancestral Indian is way off for a Pathan (I remember telling me that you are a Pathan and Tajik). It's weird, very, very weird.


It's a Gedrosia calculator. The last one in the list.

I am not Pashtun/Tajik. I think you may be thinking of Rukha.
I am Saraiki-Baloch, Kashmiri, Kho, Uzbek.

My uncle and I were in the original run when Kurd made the calculator, so it's likely there is a calculator effect going on. Because those of us in the run score pretty high ASI relative to those who weren't in the run.
Either way, I am going to score more ASI than a Pathan or Tajik any day.

Xehanort
10-11-2017, 06:40 PM
It's a Gedrosia calculator. The last one in the list.

I am not Pashtun/Tajik. I think you may be thinking of Rukha.
I am Saraiki-Baloch, Kashmiri, Kho, Uzbek.

My uncle and I were in the original run when Kurd made the calculator, so it's likely there is a calculator effect going on. Because those of us in the run score pretty high ASI relative to those who weren't in the run.
Either way, I am going to score more ASI than a Pathan or Tajik any day.

Yeah, thanks for clarifying. I certainly agree with you, and sorry for the confusion.

One last thing, why do Punjabis from Lahore score such a high degree of ASI, which is even comparable to Tamils and many other South Indians, whereas Punjabi Jatts, Gujjars, Rajputs, etc., do not, and are more in line with Sindhis and to a lesser extent, Pathans? Is there a reason for this discrepancy? Could it be that the PJL samples are those of Chamars?

MonkeyDLuffy
10-11-2017, 09:03 PM
Yeah, thanks for clarifying. I certainly agree with you, and sorry for the confusion.

One last thing, why do Punjabis from Lahore score such a high degree of ASI, which is even comparable to Tamils and many other South Indians, whereas Punjabi Jatts, Gujjars, Rajputs, etc., do not, and are more in line with Sindhis and to a lesser extent, Pathans? Is there a reason for this discrepancy? Could it be that the PJL samples are those of Chamars?

Punjabi Lahore samples are very mixed samples. Majority of them are lower caste converts who converted to Islam to escape the caste system in Hinduism. Hence they have higher ASI or native south asian ancestry. Good amount of SA muslims, are converts from lower castes. The same thing that's happening nowdays, but this time its christianity.

Xehanort
10-12-2017, 12:40 AM
Punjabi Lahore samples are very mixed samples. Majority of them are lower caste converts who converted to Islam to escape the caste system in Hinduism. Hence they have higher ASI or native south asian ancestry. Good amount of SA muslims, are converts from lower castes. The same thing that's happening nowdays, but this time its christianity.

Thanks, are Gujjars high caste? I used to think that Gujjars were low caste converts until I saw their DNA results, and they're similar to Brahmins, Jatts, and Rajputs. It is pretty surprising, indeed.

MonkeyDLuffy
10-12-2017, 02:38 AM
Thanks, are Gujjars high caste? I used to think that Gujjars were low caste converts until I saw their DNA results, and they're similar to Brahmins, Jatts, and Rajputs. It is pretty surprising, indeed.

Gujjars, jats, kamboj, Sainis etc never were part of Hindu caste system, they have their own hierarchy. Hence their results are different. They popped up in SA with different waves of invasions and migrations.

Xehanort
10-12-2017, 02:43 AM
Gujjars, jats, kamboj, Sainis etc never were part of Hindu caste system, they have their own hierarchy. Hence their results are different. They popped up in SA with different waves of invasions and migrations.

Alright, thanks for clarifying. Appreciate it! :)

Xehanort
10-12-2017, 03:53 AM
Admix Results (sorted):

# Population Percent
1 IRAN_NEOLITHIC 36.11
2 CHG_EEF 22.86
3 NATUFIAN 14.38
4 ANATOLIA_NEOLITHIC 12.51
5 ANCESTRAL_INDIAN 5.54
6 EHG 4.81
7 SIBERIAN 1.79
8 PAPUAN 1.26
9 SUB_SAHARAN 0.74

Do you know why Iranians have less Neolithic Iranian DNA than Zoroastrians, and the recent Iran sample as well?

MonkeyDLuffy
10-12-2017, 01:49 PM
Do you know why Iranians have less Neolithic Iranian DNA than Zoroastrians, and the recent Iran sample as well?

Because Zoroastrians mixed less during introduction of Islam to the region because of their religion. Hence they preserved the native admixture more.

Xehanort
10-12-2017, 04:41 PM
Because Zoroastrians mixed less during introduction of Islam to the region because of their religion. Hence they preserved the native admixture more.

I know but, how admixed do you think modern Iranians are compared to Ancient Iranians?

DMXX
10-12-2017, 05:44 PM
It isn't going to be due to post-Islamic admixture; we have historical data showing Arab introgression into the plateau was limited to the Sassanid administrative or royal classes, many of whom were killed or fled Iran in subsequent revolts. That is another strange misconception about Iran's Medieval history which refuses to die (we never needed genetics to confirm this).

Zoroastrians are more Iran_N than Iranians from the north because of autochthonous prehistoric heritage patterns (I explained this in my earlier post). Iranians from Bandar Abbas, Shiraz and Balochis are all more Iran_N shifted than Iranians from the northwest (including Kurds) and the Caspian coastline (Mazandaranis). The further northwest you go in Iran, the more EEF-related ancestry. The further southeast, the more Iran_N. Formal stats, from both genome bloggers and publications, show that trend.

There appears to be variation among the Chalcolithic Iranian samples regarding the proportions of Iran_N and EEF-related ancestry, so the bulk of the difference between your generic Mazandarani and Zoroastrian could be comfortably attributed to the above.

Xehanort
10-12-2017, 06:55 PM
It isn't going to be due to post-Islamic admixture; we have historical data showing Arab introgression into the plateau was limited to the Sassanid administrative or royal classes, many of whom were killed or fled Iran in subsequent revolts. That is another strange misconception about Iran's Medieval history which refuses to die (we never needed genetics to confirm this).

Zoroastrians are more Iran_N than Iranians from the north because of autochthonous prehistoric heritage patterns (I explained this in my earlier post). Iranians from Bandar Abbas, Shiraz and Balochis are all more Iran_N shifted than Iranians from the northwest (including Kurds) and the Caspian coastline (Mazandaranis). The further northwest you go in Iran, the more EEF-related ancestry. The further southeast, the more Iran_N. Formal stats, from both genome bloggers and publications, show that trend.

There appears to be variation among the Chalcolithic Iranian samples regarding the proportions of Iran_N and EEF-related ancestry, so the bulk of the difference between your generic Mazandarani and Zoroastrian could be comfortably attributed to the above.

Thanks, and I certainly agree with your observation here. However, some Iranian populations do seem to have significant foreign admixture, although, none of it seems to be Arab, of course. The Arab genetic impact on Iran was virtually nil, and the Jewish impact could have been greater as many Jews converted to Islam after the arrival of the Arabs, and likely intermingled with the local population. Jews are shown to have more Semitic/Arabian admixture than other Iranian populations, likely due to their origin as a Semitic peoples. Another population which is significantly mixed is the Bandari people, who are outlier in the Iranian gene pool due to their significant South Asian and African admixture. Thus, it is my understanding that Iranian Jews, Iranian Bandaris, and even Iranian Arabs cannot be considered an wholly Iranic population. The same can be said about Iranian Azeris and Iranian Turkmen, both of which have significant Mongoloid admixture, although it is much more limited in the Azeris (5 to 15%). Azerbaijanis from Azerbaijan are certainly a whole different case, as they are more similar to Armenians and Georgians. Overall, however, I feel that the Iranian population has largely remained stable, but there does seem to be an influx of South Asian and Mongoloid genes since the 14th century, minor African admixture as well in some cases (Of course the South Asian could be hidden Neolithic Iranian admixture). I appreciate your reply! I was also wondering though, aren't many Caspians mixed with Georgians and Armenians? I remember that Shah Abbas imported a lot of Georgian and Armenians into his empire, although at the time this would have account for only about 2% of Iran's population (200,000 out of 12,000,000). Unfortunately, the Iranian population declined significantly following the fall of the Safavid dynasty and the rise of Nader Shah and his wars of conquest (12,000,000 to 1,400,000).

Agamemnon
10-13-2017, 12:28 AM
Iranian Jews are Mizrahi, much like Iraqi, Kurdish, Georgian and Uzbek Jews they are principally Mesopotamian in origin, in fact they plot with Assyrians and Mandaeans on most PCAs I've seen.

Xehanort
10-13-2017, 01:56 AM
Iranian Jews are Mizrahi, much like Iraqi, Kurdish, Georgian and Uzbek Jews they are principally Mesopotamian in origin, in fact they plot with Assyrians and Mandaeans on most PCAs I've seen.

Interesting, thanks for the reply. Are you a Romaniote Jew? Or are you Ashkenazi? Your use of Greek suggests the latter. In terms of your Y-DNA and MtDNA, you're as Jewish as it gets. Pretty much a Cohenim in my opinion.

Agamemnon
10-13-2017, 09:09 PM
Interesting, thanks for the reply. Are you a Romaniote Jew? Or are you Ashkenazi? Your use of Greek suggests the latter. In terms of your Y-DNA and MtDNA, you're as Jewish as it gets. Pretty much a Cohenim in my opinion.

No, I am not a Romaniote Jew. My father is mainly Ashkenazi (from Belarus and Ukraine/Crimea), he has some distant Syrian Jewish and Iranian Jewish ancestry (as well as very distant Samaritan ancestry, this shows up consistently). My mother is British (English, Scottish, Welsh, Manx). Indeed, my paternal lineage is the famous "Cohen Modal Haplotype (https://en.wikipedia.org/wiki/Y-chromosomal_Aaron)" (you could call J1-Z18271 the "Cohen Modal SNP" for that matter), my mtDNA haplogroup hasn't got much to do with the Jews though (it was found in two Corded Ware samples and one Bell Beaker sample).

Xehanort
10-14-2017, 03:48 AM
No, I am not a Romaniote Jew. My father is mainly Ashkenazi (from Belarus and Ukraine/Crimea), he has some distant Syrian Jewish and Iranian Jewish ancestry (as well as very distant Samaritan ancestry, this shows up consistently). My mother is British (English, Scottish, Welsh, Manx). Indeed, my paternal lineage is the famous "Cohen Modal Haplotype (https://en.wikipedia.org/wiki/Y-chromosomal_Aaron)" (you could call J1-Z18271 the "Cohen Modal SNP" for that matter), my mtDNA haplogroup hasn't got much to do with the Jews though (it was found in two Corded Ware samples and one Bell Beaker sample).

Oh, alright. Thanks for clarifying. I always found it interesting how Ashkenazi Jews managed to maintain their paternal Jewish lineage, despite centuries of separation from their ancestral homeland in the Middle East.

Agamemnon
10-14-2017, 03:39 PM
Oh, alright. Thanks for clarifying. I always found it interesting how Ashkenazi Jews managed to maintain their paternal Jewish lineage, despite centuries of separation from their ancestral homeland in the Middle East.

You are quite right, for instance the fact that my paternal lineage is found in Kohanim from virtually every Jewish community (including Mizrahi Jews) is quite impressive, this tells us priestly status was taken very seriously by the Jews. IMO the fact that Ashkenazi and other Western Jews (French, Italian, Romaniote, Sephardic, North African & Syro-Lebanese Jews) still form a single population from a genetic standpoint after nearly 2,000 years of exile is even more impressive, this bears testimony to the Jewish people's resilience in a sense.

Anyway, sorry for the off-topic digression!

Xehanort
10-14-2017, 04:04 PM
You are quite right, for instance the fact that my paternal lineage is found in Kohanim from virtually every Jewish community (including Mizrahi Jews) is quite impressive, this tells us priestly status was taken very seriously by the Jews. IMO the fact that Ashkenazi and other Western Jews (French, Italian, Romaniote, Sephardic, North African & Syro-Lebanese Jews) still form a single population from a genetic standpoint after nearly 2,000 years of exile is even more impressive, this bears testimony to the Jewish people's resilience in a sense.

Anyway, sorry for the off-topic digression!

No worries. I appreciate your comments and feedback. Thank you :). It's been a pleasure talking to you! And you're right, this is exactly why the Jewish people were able to maintain their lineage. I was wondering, though, why do eastern Jews (Iranian, Yemeni, Iraqi, Bukharan, Indian) form a separate cluster than western Jews?

Agamemnon
10-14-2017, 10:44 PM
No worries. I appreciate your comments and feedback. Thank you :). It's been a pleasure talking to you! And you're right, this is exactly why the Jewish people were able to maintain their lineage. I was wondering, though, why do eastern Jews (Iranian, Yemeni, Iraqi, Bukharan, Indian) form a separate cluster than western Jews?

You're welcome :) Regarding your question, the answer is rather simple really. Mizrahi/Eastern Jews form a separate population mainly because they are by and large of Mesopotamian origin, and Mesopotamia had the oldest Jewish communities outside the land of Israel (though Egypt also happens to be a serious contender). Jews have lived in Mesopotamia at least since the last 2,500 years, that is to say long before the laws regulating intermarriage appeared, moreover they had plenty of time to mingle with their host population (Jewishness was transmitted patrilineally prior to the Tanna'im, this would explain why the paternal lineages tend to be shared with Western Jews despite the different cluster they form). IMO the genetic dichotomy between Eastern and Western Jews reflects Aramaic and Greek-speaking Jewry more than anything else.

DMXX
10-15-2017, 12:12 PM
Thanks, and I certainly agree with your observation here. However, some Iranian populations do seem to have significant foreign admixture, although, none of it seems to be Arab, of course. The Arab genetic impact on Iran was virtually nil, and the Jewish impact could have been greater as many Jews converted to Islam after the arrival of the Arabs, and likely intermingled with the local population. Jews are shown to have more Semitic/Arabian admixture than other Iranian populations, likely due to their origin as a Semitic peoples. Another population which is significantly mixed is the Bandari people, who are outlier in the Iranian gene pool due to their significant South Asian and African admixture. Thus, it is my understanding that Iranian Jews, Iranian Bandaris, and even Iranian Arabs cannot be considered an wholly Iranic population. The same can be said about Iranian Azeris and Iranian Turkmen, both of which have significant Mongoloid admixture, although it is much more limited in the Azeris (5 to 15%). Azerbaijanis from Azerbaijan are certainly a whole different case, as they are more similar to Armenians and Georgians. Overall, however, I feel that the Iranian population has largely remained stable, but there does seem to be an influx of South Asian and Mongoloid genes since the 14th century, minor African admixture as well in some cases (Of course the South Asian could be hidden Neolithic Iranian admixture). I appreciate your reply! I was also wondering though, aren't many Caspians mixed with Georgians and Armenians? I remember that Shah Abbas imported a lot of Georgian and Armenians into his empire, although at the time this would have account for only about 2% of Iran's population (200,000 out of 12,000,000). Unfortunately, the Iranian population declined significantly following the fall of the Safavid dynasty and the rise of Nader Shah and his wars of conquest (12,000,000 to 1,400,000).

Iranians, by and large, haven't changed substantially since the Iron Age. That is the central conclusion that must not be overshadowed by any emphasis of the differences between modern Iranian populations.

There has, however, been significant admixture through additional sources since the Iron Age in select populations. As you highlighted, there is East Eurasian admixture across most of the plateau (though it seems to only exceed 2% in northern populations). The most reliable vector for this is through the Turkish migrations. There is also Sub Saharan admixture across the southern half of the plateau, and the most reliable vector is likely going to be the Islamic slave trade. From what can be inferred through the ADMIXTURE-derived Oracle results, the absolute majority of Iranians are at least 90% of the "same stuff" as their ancestral kin.
Whether the remaining 10% grants different individuals an outlier status is admittedly arbitrary. As an example, am I an "outlier" when I score 89% Iranian 11% European in the Oracles? Up for debate, though I'm not convinced that debate (and the underlying urgency to concretely define what constitutes an outlier vs. conventional) is worth the time taken.

There probably are a sizable (arbitrary guess - 5-10,000 people?) number of Iranians with substantial admixture from the Arabian peninsula. Some of the Behar et al. Iranians have a full 1 SD greater "SW Asian"-related component scores compared to others in that sample set. However, we don't have any formal stats to show whether that is in fact Arabian ancestry, or instead, surplus BE affinity (the indigenous Iranian farmers were more BE than modern Iranians). If I were to hazard a guess, those Iranians with Arabian ancestry would mostly be among the religious class (recall their somewhat endogamous subculture and frequent pairing with Muslims elsewhere in the Islamic world, particularly in Iraq) or the southern coastal towns.

Many people from northern Iran have ancestry from the Caucasus, yes. The degree appears to vary. Some have recent known admixture (e.g. NK19191 on this forum, who is a quarter Georgian), others have very distant connections (such as myself; I'm nothing but Azeri Iranian or Persian on both sides going back 5-6 generations).

Xehanort
10-15-2017, 04:10 PM
Iranians, by and large, haven't changed substantially since the Iron Age. That is the central conclusion that must not be overshadowed by any emphasis of the differences between modern Iranian populations.

There has, however, been significant admixture through additional sources since the Iron Age in select populations. As you highlighted, there is East Eurasian admixture across most of the plateau (though it seems to only exceed 2% in northern populations). The most reliable vector for this is through the Turkish migrations. There is also Sub Saharan admixture across the southern half of the plateau, and the most reliable vector is likely going to be the Islamic slave trade. From what can be inferred through the ADMIXTURE-derived Oracle results, the absolute majority of Iranians are at least 90% of the "same stuff" as their ancestral kin.
Whether the remaining 10% grants different individuals an outlier status is admittedly arbitrary. As an example, am I an "outlier" when I score 89% Iranian 11% European in the Oracles? Up for debate, though I'm not convinced that debate (and the underlying urgency to concretely define what constitutes an outlier vs. conventional) is worth the time taken.

There probably are a sizable (arbitrary guess - 5-10,000 people?) number of Iranians with substantial admixture from the Arabian peninsula. Some of the Behar et al. Iranians have a full 1 SD greater "SW Asian"-related component scores compared to others in that sample set. However, we don't have any formal stats to show whether that is in fact Arabian ancestry, or instead, surplus BE affinity (the indigenous Iranian farmers were more BE than modern Iranians). If I were to hazard a guess, those Iranians with Arabian ancestry would mostly be among the religious class (recall their somewhat endogamous subculture and frequent pairing with Muslims elsewhere in the Islamic world, particularly in Iraq) or the southern coastal towns.

Many people from northern Iran have ancestry from the Caucasus, yes. The degree appears to vary. Some have recent known admixture (e.g. NK19191 on this forum, who is a quarter Georgian), others have very distant connections (such as myself; I'm nothing but Azeri Iranian or Persian on both sides going back 5-6 generations).

I see, thanks for your reply. I do think that Bandaris are outliers, since they have around 6 to 10% African ancestry, and 20 to 30% South Asian admixture. They also don't look very Iranic, compared to the other Iranian populations. Bandaris are basically South Asians, and cluster the closest with Pakistani Makranis. In fact, most Bandaris are descended from Indian and African slaves who were imported to the Iranian Plateau by the Portuguese. The Subsaharan African in Iranians is over estimated in my opinion, and in reality it is virtually absent in the majority of Iranians. The Behar et. al Iranians were likely Bandaris. I think that most studies need to be done on Ancient Iranians. We still lack samples from the Sassanid era.

Xehanort
10-15-2017, 04:12 PM
You're welcome :) Regarding your question, the answer is rather simple really. Mizrahi/Eastern Jews form a separate population mainly because they are by and large of Mesopotamian origin, and Mesopotamia had the oldest Jewish communities outside the land of Israel (though Egypt also happens to be a serious contender). Jews have lived in Mesopotamia at least since the last 2,500 years, that is to say long before the laws regulating intermarriage appeared, moreover they had plenty of time to mingle with their host population (Jewishness was transmitted patrilineally prior to the Tanna'im, this would explain why the paternal lineages tend to be shared with Western Jews despite the different cluster they form). IMO the genetic dichotomy between Eastern and Western Jews reflects Aramaic and Greek-speaking Jewry more than anything else.

Thanks for answering my inquiry. Do most Eastern Jews have J1 or J2 as their Y-DNA? I would assume it's the latter. Also, are Yemeni Jews likely descendants of Yemeni converts?

ancestryfan1994
10-15-2017, 04:16 PM
I'd like to piggy back on DMXX's comments above, the comment on Iranians being for the most part 90% similar to their ancient ancestors holds very true from what I've seen both personally from my own families genetic profile, and other Iranians. Even though my family fall on both spectrums of what is an outlier, and what is deemed to be representative of this similarity to the old school Iranians. I can confirm that we are also 80-90% Persian, and if my memory serves me right, clustered pretty close to some of the ancient and modern Iranian samples in PCA plots made by Davidski, and more recently a large forum member plot by the user khanabadoshi. The last 10% of admixture for my family however, would be deemed a pretty major outlier, consisting of a complex cluster of different things, but for the most part, we fall in line with other Iranians.

The actual Arabian ancestry also varies in Iran, I remember people claiming Arab heritage in the south of Iran, most were recent transplants from Iraq that flooded in after the war, there's even a couple half arabs in our immediate family/friends, whether they be married in, or a wife of a friend etc. But I don't know if these Arabs that blended in with the communities in Iran are genuine Arab from say, Arab Bedouin tribes, or just Arabized Iranians, because I remember seeing an Iranian "Arab" on GEDmatch that genetically turned out to be the same as other Iranians.

ancestryfan1994
10-15-2017, 04:20 PM
I see, thanks for your reply. I do think that Bandaris are outliers, since they have around 6 to 10% African ancestry, and 20 to 30% South Asian admixture. They also don't look very Iranic, compared to the other Iranian populations. Bandaris are basically South Asians, and cluster the closest with Pakistani Makranis. In fact, most Bandaris are descended from Indian and African slaves who were imported to the Iranian Plateau by the Portuguese. The Subsaharan African in Iranians is over estimated in my opinion, and in reality it is virtually absent in the majority of Iranians. The Behar et. al Iranians were likely Bandaris. I think that most studies need to be done on Ancient Iranians. We still lack samples from the Sassanid era.

Its important to define the term Bandari? are you speaking of all Iranians from the coastal areas?

Being that I'm a southern Iranian, my Iranian matches are almost exclusively from the southern port cities, and never have they had SSA admixture that exceeds 1-2%, the only Iranians I've seen with that much SSA are ones from the gulf states, and I would imagine there is a pocket or Iranians that have large sums of SSA, but they're most likely remnants of the afro Iranian community, which isn't that large to begin with, but still exists today.

Xehanort
10-15-2017, 05:08 PM
Its important to define the term Bandari? are you speaking of all Iranians from the coastal areas?

Being that I'm a southern Iranian, my Iranian matches are almost exclusively from the southern port cities, and never have they had SSA admixture that exceeds 1-2%, the only Iranians I've seen with that much SSA are ones from the gulf states, and I would imagine there is a pocket or Iranians that have large sums of SSA, but they're most likely remnants of the afro Iranian community, which isn't that large to begin with, but still exists today.

Bandari as in from Hormozgan, specifically Bandar Abbas, and other coastal areas in the south of Iran. All the Bandari samples I have seen are at least 6% SSA and 25% Indian. Shirazis are not Bandaris, and are actually similar to other Iranians. By Bandari I am not referring to southern Iranians in general, but specifically those from Bandar Abbas, and its surrounding regions.

Xehanort
10-15-2017, 05:10 PM
I'd like to piggy back on DMXX's comments above, the comment on Iranians being for the most part 90% similar to their ancient ancestors holds very true from what I've seen both personally from my own families genetic profile, and other Iranians. Even though my family fall on both spectrums of what is an outlier, and what is deemed to be representative of this similarity to the old school Iranians. I can confirm that we are also 80-90% Persian, and if my memory serves me right, clustered pretty close to some of the ancient and modern Iranian samples in PCA plots made by Davidski, and more recently a large forum member plot by the user khanabadoshi. The last 10% of admixture for my family however, would be deemed a pretty major outlier, consisting of a complex cluster of different things, but for the most part, we fall in line with other Iranians.

The actual Arabian ancestry also varies in Iran, I remember people claiming Arab heritage in the south of Iran, most were recent transplants from Iraq that flooded in after the war, there's even a couple half arabs in our immediate family/friends, whether they be married in, or a wife of a friend etc. But I don't know if these Arabs that blended in with the communities in Iran are genuine Arab from say, Arab Bedouin tribes, or just Arabized Iranians, because I remember seeing an Iranian "Arab" on GEDmatch that genetically turned out to be the same as other Iranians.

I agree, you're right for the most part. The Arab admixture in Iranians is highly exaggerated. Heck, Iranians are more South Asian than they are Arab. I don't know why this myth is still around because it's not true, at all. Most of the Arabs who settled in Iran, settled in Iranian Central Asia, specifically Khorassan. And they likely left no trace as the Mongols sacked and razed nearly all Iranian cities in Central Asia.

Lupus82
10-15-2017, 05:17 PM
Did you happen to analyze the genetical differences between Iranians and Kurds? (Especially the Kurds who do not live inside the modern borders of Iran) I wonder your thoughts.

pegasus
10-15-2017, 08:48 PM
I know but, how admixed do you think modern Iranians are compared to Ancient Iranians?

I think they have maintained a steady strong link with Chalcolithic Iranians who displaced the earlier Neolithic Iranians. Plateau Iranians to me are like SW Asian shifted Caucasus populations, the overwhelming portion of their ancestry is CHG not Iran_N/Hotu, even in those results , a good chunk of the Iran_N is actually CHG. Which makes sense the population which brought Iran_Chl to the Iranian Plateau came west of the Zagros with Halaf farmers in Eastern Anatolia/Northern Iraq, and plateau Iranians cluster very closely with Eastern Anatolians even today.

pegasus
10-15-2017, 08:55 PM
Bandari as in from Hormozgan, specifically Bandar Abbas, and other coastal areas in the south of Iran. All the Bandari samples I have seen are at least 6% SSA and 25% Indian. Shirazis are not Bandaris, and are actually similar to other Iranians. By Bandari I am not referring to southern Iranians in general, but specifically those from Bandar Abbas, and its surrounding regions.

Southern Iranians have South Asian affinity by virtue of the fact that unlike other plateau Iranians, their base ancestry is still Iran_N, while for plateau Iranians its CHG.

Xehanort
10-15-2017, 10:08 PM
I think they have maintained a steady strong link with Chalcolithic Iranians who displaced the earlier Neolithic Iranians. Plateau Iranians to me are like SW Asian shifted Caucasus populations, the overwhelming portion of their ancestry is CHG not Iran_N/Hotu, even in those results , a good chunk of the Iran_N is actually CHG. Which makes sense the population which brought Iran_Chl to the Iranian Plateau came west of the Zagros with Halaf farmers in Eastern Anatolia/Northern Iraq, and plateau Iranians cluster very closely with Eastern Anatolians even today.

Actually, to be honest, Chalcolithic Iranians were just Neolithic Iranians with minor admixture from Neolithic Anatolians. I don't think that they completely forced Neolithic Iranians out.

Xehanort
10-15-2017, 10:09 PM
Southern Iranians have South Asian affinity by virtue of the fact that unlike other plateau Iranians, their base ancestry is still Iran_N, while for plateau Iranians its CHG.

Yes, but Iran_N does not equal ASI. They're two completely different populations. Although, Pakistanis and Indians are heavily influenced by Iran_N.

pegasus
10-15-2017, 11:25 PM
Actually, to be honest, Chalcolithic Iranians were just Neolithic Iranians with minor admixture from Neolithic Anatolians. I don't think that they completely forced Neolithic Iranians out.

Not really. They are called Iran_Chl but reality is they are largely a farming community which lived West of the Zagros and are intrusive to the Iranian plateau but definitely absorbed extra Iran_N but the fact is they largely displaced the Iran_N/Hotu populations . Levantines and other near easterners have a huge amount of Iran_Chl ancestry. Plateau Iranians have a good amount of ANF as well Natufian related stuff. Thats why Plateau Iranians cluster so well with Eastern Anatolians, they more or less descend from the same people . Iran_Chl is mainly CHG not Iran_N, Iran_N is like 15% and the rest is Levantine/Natufian related.

pegasus
10-15-2017, 11:28 PM
Yes, but Iran_N does not equal ASI. They're two completely different populations. Although, Pakistanis and Indians are heavily influenced by Iran_N.

Iran_N/Hotu ancestry peaks in NW South Asians not in Plateau Iranians. ASI is the ENA portion of S/SC populations populations.

Kurd
10-17-2017, 08:38 PM
IranN peaks in Iranic peoples. I took a little detour from work to do an allele by allele comparison (IBS) using PLINK. Broushaki had mentioned Zoroastrians and Baloch. Here are some other Iranian groups (Mazenderanis, Zoroastrians, Kurds, Parsis, SW Iranians, Balochis, and Makranis) along with a few project members thrown in. The IBS results show that Iranics top the list for allele sharing with both neolithic samples, Ganj Dareh and Wegmah Cave.

Keep in mind that the ordering will change a little once I dipolid process the samples, because pseudo-haploid ones, such as the ones published, are ill suited for IBS/IBD work.

This is consistent with the K12 Ancient Calculator ADMIXTURE calculator results. However, Gedmatch based calculators should not be relied upon for reasons I have previously discussed, the main ones include that the IranN cluster is very weak because there are only 2 samples, so what ends up happening is it turns into a predominantly S Asian cluster because of all the S Asians that gang up under it (not that different from S Asians scoring high C Asian, because they have no choice because the only other comp that describes their sub-structure is S Indian, whereas W Asians have plenty of choices in terms of W Asian and SE European comps, so they usually get pushed off to another comp). In other words, Gedmatch based calculators are highly dependent on which non-reference samples get tossed into the run.

E Pakistanis/Indians are further down the list because they don't share as many alleles with IranN as the aforementioned. This shows continuity since the neolithic in Iran. Sometime during or after the neolithic individuals related to IranN migrated from the Kurdistan area in Iran to SC/S Asia at various times. This allowed for a diffusion of the modal comp throughout the area. The reason that Baloch show elevated levels compared with E Pakistanis/Indians, is that they are relatively recent split from Kurds/W Iranians.

Any theory that contradicts this needs to 1st explain why W Iranians share such a large number of alleles with IranN.



SAMPLE
ID
Iran_N_GanjDareh


Iran_N
I1290
100.000%


Iran_n_WC1
WC1
65.823%


Balochi
HGDP00074
65.309%


Iranian
SHII72
65.282%


Makrani
HGDP00133
65.253%


Iran_Zoroastrian
YZ037
65.252%


Iranian_Bandari
BanII40
65.239%


Iranian
GMII22
65.233%


Iran_Zoroastrian
YZ020
65.167%


Iranian
SHII20
65.166%


Balochi
HGDP00052
65.162%


Kurd_N
kurd1156
65.155%


Makrani
HGDP00155
65.132%


Iranian
LORII36
65.123%


Iran_Zoroastrian
YZ039
65.118%


Iranian
LORII48
65.112%


Makrani
HGDP00135
65.111%


Iran_Zoroastrian
SH003
65.104%


Balochi
HGDP00064
65.102%


Iranian
GMII54
65.098%


Iranian
GMII19
65.093%


Iran_recent
I1955
65.090%


Iran_Fars
IREJ-T184
65.085%


Iranian
iran16
65.084%


Iranian_Bandari
BanII47
65.083%


.NK19191
ID001
65.082%


Balochi
HGDP00096
65.079%


.Znertu
ID001
65.073%


Georgian
mg49
65.071%


Iran_Zoroastrian
T006
65.070%


Iranian
iran3
65.069%


.Kurd_F6
ID001
65.058%


Makrani
HGDP00160
65.057%


Iranian
LORII51
65.050%


Kurd_N
kurd1159
65.050%


Balochi
HGDP00062
65.046%


Iranian
iran2
65.044%


Iran_Fars
IREJ-T023
65.041%


Makrani
HGDP00158
65.038%


Kurd_N
kurd1173
65.036%


Makrani
HGDP00131
65.035%


Baloch_IR2
ID001
65.031%


Iran_Zoroastrian
T016
65.028%


Iran_Zoroastrian
T013
65.021%


Iranian
GMII79
65.021%


Iran_Zoroastrian
T012
65.018%


Iranian
SHII27
65.013%


Baloch_IR1
ID001
65.010%


Iranian
GMII7
65.009%


Makrani
HGDP00154
65.002%


Iranian
GMII16
65.001%


Iranian
GMII18
64.994%


Iran_Zoroastrian
I002
64.993%


Iranian
GMII20
64.991%


.Kurd_F8
ID001
64.990%


Iran_Zoroastrian
YZ022
64.988%


Balochi
HGDP00066
64.983%


Iran_Zoroastrian
I001
64.980%


Pakistan_Parsi
EGYPTLC5544390
64.979%


Pakistan_Parsi
EGYPTLC5544384
64.977%


Iran_Zoroastrian
YZ035
64.977%


Makrani
HGDP00137
64.975%


Pathan
HGDP00264
64.974%


Makrani
HGDP00146
64.966%


Balochi
HGDP00092
64.965%


Iran_Fars
IREJ-T078
64.963%


.Mfa
ID001
64.963%


Iranian
LORII52
64.963%


Iranian
GMII29
64.961%


Iranian_Bandari
BanII90
64.961%


Georgian
mg40
64.961%


Iran_Fars
IREJ-T053
64.960%


Iran_Zoroastrian
T010
64.959%


Pakistan_Parsi
EGYPTLC5544385
64.957%


.Zephyrous
ID001
64.953%


Makrani
HGDP00157
64.953%


.Hanna
ID001
64.949%


Iranian
GMII36
64.947%


.Kurd_F7
ID001
64.946%


Makrani
HGDP00145
64.938%


Iran_Zoroastrian
T015
64.933%


Makrani
HGDP00153
64.932%


Pakistan_Parsi
EGYPTLC5544393
64.924%


Iranian
LORII44
64.923%


Iranian
iran19
64.922%


GujaratiA
NA20862
64.922%


Pakistan_Parsi
EGYPTLC5544391
64.919%


Kalash
HGDP00311
64.918%


Kalash
HGDP00328
64.917%


Iran_Fars
IREJ-T103
64.916%


Iran_Fars
IREJ-T037
64.914%


Balochi
HGDP00080
64.913%

Kurd
10-17-2017, 08:40 PM
cont



Iran_Zoroastrian
SH005
64.912%


Iranian
LORII19
64.905%


Balochi
HGDP00098
64.905%


Makrani
HGDP00141
64.903%


.Kurd_F4
ID001
64.899%


Iranian
LORII34
64.895%


Makrani
HGDP00134
64.893%


Iranian
iran17
64.890%


Iranian
LORII50
64.890%


.Halgurd
ID001
64.889%


Iranian_Bandari
BanII38
64.887%


Iran_Zoroastrian
YZ019
64.885%


Iran_Fars
IREJ-T022
64.884%


Pakistan_Parsi
EGYPTLC5544403
64.884%


Iranian
SHII25
64.884%


Iranian
SHII87
64.883%


Pakistan_Parsi
EGYPTLC5544395
64.879%


Balochi
HGDP00072
64.879%


.Kurd_F1
ID001
64.878%


.Kurd_F5
ID001
64.877%


Iranian
SHII66
64.871%


Iran_Fars
IREJ-T009
64.868%


Iran_Fars
IREJ-T064
64.866%


Balochi
HGDP00078
64.866%


Pathan
HGDP00222
64.863%


Makrani
HGDP00140
64.861%


Iran_Fars
IREJ-T090
64.860%


Pakistan_Parsi
EGYPTLC5544396
64.858%


Makrani
HGDP00136
64.856%


Iranian
SHII91
64.854%


.Kurd_C2
ID001
64.852%


Iran_Fars
IREJ-T204
64.850%


Balochi
HGDP00082
64.847%


Iran_Zoroastrian
T011
64.843%


Pakistan_Parsi
EGYPTLC5544401
64.842%


Pathan
HGDP00262
64.841%


Pakistan_Parsi
EGYPTLC5544383
64.840%


Kalash
HGDP00298
64.836%


Kurd_N
kurd1198
64.835%


.Kurd_C7
ID001
64.835%


Balochi
HGDP00086
64.833%


Kurd_N
kurd1160
64.832%


Iranian_Bandari
BanII4
64.832%


Kalash
HGDP00290
64.830%


Iran_Zoroastrian
T007
64.829%


Iran_Zoroastrian
SH007
64.822%


Iran_Fars
IREJ-T027
64.821%


Georgian
mg23
64.820%


Iran_Zoroastrian
SH001
64.819%


Iran_Fars
IREJ-T040
64.817%


Georgian
mg31
64.814%


.Kurd_F2
ID001
64.813%


Pakistan_Parsi
EGYPTLC5544388
64.813%


Iranian
SHII51
64.812%


.Kurd_F3
ID001
64.812%


Iran_Zoroastrian
T003
64.810%


Kalash
HGDP00315
64.801%


Iran_Fars
IREJ-T101
64.800%


Kalash
HGDP00319
64.798%


Georgian
mg47
64.797%


Makrani
HGDP00144
64.795%


Balochi
HGDP00094
64.789%


Makrani
HGDP00151
64.787%


Pakistan_Parsi
EGYPTLC5544398
64.785%


Pakistan_Parsi
EGYPTLC5544386
64.784%


Iran_Zoroastrian
SH008
64.784%


Iranian
iran20
64.783%


Balochi
HGDP00068
64.779%


Iranian
LORII9
64.777%


Iran_Zoroastrian
YZ033
64.773%


Iran_Fars
IREJ-T026
64.770%


Iran_Zoroastrian
SH004
64.769%


Pakistan_Parsi
EGYPTLC5544402
64.766%


Georgian
mg62
64.766%


Pathan
HGDP00259
64.766%


Balochi
HGDP00088
64.762%


.Punjabi_Gujjar
ID001
64.755%


Georgian
mg22
64.753%


.Kurd_Ezidi
ID001
64.751%


Balochi
HGDP00054
64.750%


Makrani
HGDP00148
64.748%


.Punjabi_Rgh
ID001
64.744%


Pathan
HGDP00216
64.743%


Sindhi
HGDP00187
64.743%


Iranian
LORII58
64.740%


.Kurd_C6
ID001
64.738%


.Hanif
ID001
64.737%


Sindhi
HGDP00195
64.736%


Pakistan_Parsi
EGYPTLC5544394
64.734%


Balochi
HGDP00090
64.733%


Iranian
iran14
64.729%


Iran_Zoroastrian
YZ030
64.729%


.Kurd_C1
ID001
64.728%


Pakistan_Parsi
EGYPTLC5544399
64.727%


.Khana
ID001
64.724%


Iranian
iran11
64.723%


Kurd_N
kurd1101
64.720%


Sindhi
HGDP00205
64.715%


.Kurd_C8
ID001
64.714%


Pathan
HGDP00244
64.714%


Iranian
SHII94
64.713%


Sindhi
HGDP00185
64.711%


Pakistan_Parsi
EGYPTLC5544400
64.711%


Balochi
HGDP00058
64.708%


Pakistan_Parsi
EGYPTLC5544389
64.708%


Georgian
mg27
64.707%


Pathan
HGDP00213
64.704%


Pathan
HGDP00230
64.704%


Kalash
HGDP00307
64.703%


Makrani
HGDP00161
64.699%


Pakistan_Parsi
EGYPTLC5544397
64.697%


GujaratiA
NA20858
64.695%


.Punjabi_Jatt
ID001
64.695%


Georgian
mg34
64.694%


Kalash
HGDP00288
64.692%


Pathan
HGDP00224
64.691%

Kurd
10-17-2017, 08:40 PM
cont



Kalash
HGDP00330
64.691%


Pathan
HGDP00254
64.688%


.Pashtun_Afg1
ID001
64.687%


.Kurd_C3
ID001
64.684%


Iran_Fars
IREJ-T006
64.682%


Pathan
HGDP00226
64.682%


.Rukha
ID001
64.681%


Sindhi
HGDP00210
64.681%


Pathan
HGDP00228
64.678%


Saudi
SaudiA9
64.674%


Georgian
mg43
64.673%


.Kurd_C5
ID001
64.658%


Iranian
SHII37
64.657%


Iran_Zoroastrian
YZ041
64.654%


Pakistan_Parsi
EGYPTLC5544387
64.652%


Sindhi
HGDP00192
64.651%


Sindhi
HGDP00179
64.650%


Pakistan_Parsi
EGYPTLC5544405
64.649%


.Sein
ID001
64.645%


Sindhi
HGDP00201
64.645%


Sindhi
HGDP00169
64.643%


Iranian_Bandari
BanII80
64.635%


Kalash
HGDP00323
64.634%


GujaratiA
NA20904
64.630%


Balochi
HGDP00056
64.626%


Iran_Zoroastrian
YZ018
64.623%


Sindhi
HGDP00167
64.617%


Pakistan_Parsi
EGYPTLC5544404
64.615%


Sindhi
HGDP00189
64.612%


Iran_Zoroastrian
YZ021
64.608%


GujaratiB
NA20898
64.605%


GujaratiA
NA20910
64.605%


Pathan
HGDP00218
64.600%


.Targum
ID001
64.596%


Kalash
HGDP00333
64.595%


Pathan
HGDP00241
64.592%


Sindhi
HGDP00206
64.591%


.Sapporo
ID001
64.590%


Kalash
HGDP00302
64.583%


BedouinB
HGDP00649
64.572%


Iran_Fars
IREJ-T111
64.568%


BedouinB
HGDP00650
64.568%


Pathan
HGDP00247
64.568%


GujaratiA
NA20881
64.566%


Sindhi
HGDP00208
64.566%


.Pashtun_Afg2
ID001
64.565%


Sindhi
HGDP00181
64.564%


Kalash
HGDP00313
64.561%


Pakistan_Parsi
EGYPTLC5544392
64.545%


GujaratiB
NA20882
64.542%


Sindhi
HGDP00183
64.532%


Saudi
saudi1403
64.528%


.Jesus
ID001
64.522%


.McNinja
ID001
64.519%


Sindhi
HGDP00191
64.519%


Pathan
HGDP00243
64.516%


Iranian_Bandari
BanII55
64.511%


Pakistan_Parsi
EGYPTLC5544382
64.507%


Sardinian
HGDP01063
64.501%


Pathan
HGDP00232
64.499%


Pathan
HGDP00258
64.479%


GujaratiD
NA20899
64.478%


Saudi
SaudiA7
64.463%


GujaratiC
NA20903
64.459%


GujaratiB
NA20873
64.459%


Saudi
SaudiA6
64.458%


Albanian
ALB220
64.455%


BedouinB
HGDP00643
64.450%


.Parasar
ID001
64.446%


Saudi
saudi1424
64.443%


Sindhi
HGDP00171
64.423%


Pathan
HGDP00248
64.415%


Albanian
ALB212
64.409%


GujaratiD
NA20847
64.408%


Sindhi
HGDP00197
64.398%


BedouinB
HGDP00653
64.397%


Albanian
ALB191
64.393%


BedouinB
HGDP00624
64.387%


Sardinian
HGDP00672
64.385%


GujaratiC
NA21116
64.378%


.Varun
ID001
64.366%


Saudi
saudi1434
64.365%


.Sadia
ID001
64.355%


BedouinB
HGDP00616
64.354%


Albanian
ALB202
64.353%


BedouinB
HGDP00701
64.347%


Saudi
SaudiA1
64.345%


GujaratiC
NA20866
64.344%


BedouinB
HGDP00641
64.343%


GujaratiD
NA21125
64.339%


Sardinian
HGDP00667
64.330%


.Marathi1
ID001
64.324%


GujaratiB
NA20854
64.313%


GujaratiC
NA21097
64.313%


GujaratiD
NA20911
64.308%


BedouinB
HGDP00636
64.304%


BedouinB
HGDP00630
64.303%


GujaratiD
NA21123
64.296%


Iranian_Bandari
BanII30
64.295%


BedouinB
HGDP00612
64.286%


BedouinB
HGDP00618
64.278%


BedouinB
HGDP00623
64.272%


.Passa
ID001
64.266%


.Kenji
ID001
64.262%


BedouinB
HGDP00648
64.260%


GujaratiC
NA20883
64.251%


GujaratiB
NA20885
64.249%


Iran_Zoroastrian
YZ024
64.224%


BedouinB
HGDP00631
64.223%


Saudi
SaudiA5
64.222%


Belarusian
bel8s
64.196%


BedouinB
HGDP00651
64.189%


Sardinian
HGDP00674
64.176%


Sardinian
HGDP01071
64.176%


.Powell
ID001
64.160%


Sardinian
HGDP01069
64.154%


Sardinian
HGDP01066
64.151%


Sardinian
HGDP01065
64.111%


Albanian
ALB213
64.106%


Sardinian
HGDP00671
64.099%


Sardinian
HGDP00670
64.095%


Albanian
ALB230
64.095%


Sardinian
HGDP01062
64.090%


.Reza1
ID001
64.083%


Sardinian
HGDP01064
64.074%


Sardinian
HGDP01067
64.072%


Sardinian
HGDP00669
64.045%


Sardinian
HGDP00666
64.019%


Belarusian
bel23s
64.017%


Belarusian
bel43s
64.002%


Belarusian
bel30s
64.001%


Sardinian
HGDP00673
63.977%


Sardinian
HGDP01070
63.895%


.Tajik1
ID001
63.848%


Sardinian
HGDP00668
63.806%


Sardinian
HGDP01068
63.752%


Somali
Ayodo_43S
63.132%


Somali
Ayodo_52S
63.058%


Somali
Ayodo_21S
63.011%


Somali
Ayodo_61S
62.942%


Somali
Ayodo_40S
62.918%


Somali
Ayodo_5S
62.835%


Somali
Ayodo_41S
62.774%


Somali
Ayodo_35S
62.599%


Somali
Ayodo_34S
62.542%


Somali
Ayodo_23S
62.527%

Kurd
10-17-2017, 08:41 PM
This IBS is for WC1



SAMPLE
ID
Iran_N_WC1


Iran_n_WC1
WC1
100.000%


Iranian
GMII16
70.947%


Iran_Fars
IREJ-T078
70.851%


Iranian
GMII79
70.849%


Iran_Zoroastrian
YZ020
70.793%


Iranian
GMII36
70.780%


Iranian
LORII36
70.765%


Iranian
LORII48
70.732%


Iranian
GMII22
70.731%


Kurd_N
kurd1198
70.729%


Iranian
GMII29
70.708%


Balochi
HGDP00080
70.687%


Iranian
LORII9
70.668%


Iranian_Bandari
BanII40
70.667%


Pathan
HGDP00218
70.637%


Iranian_Bandari
BanII38
70.635%


Iran_Zoroastrian
T010
70.635%


Iran_Fars
IREJ-T023
70.632%


Georgian
mg40
70.631%


Iran_Fars
IREJ-T184
70.630%


.Mfa
ID001
70.629%


Iran_Fars
IREJ-T204
70.628%


Makrani
HGDP00155
70.622%


.Kurd_F8
ID001
70.621%


Iranian
SHII27
70.617%


Iran_Fars
IREJ-T040
70.614%


Iranian
SHII37
70.600%


Iranian
GMII18
70.600%


Iranian
SHII66
70.595%


.Halgurd
ID001
70.591%


Balochi
HGDP00056
70.590%


Pathan
HGDP00222
70.584%


Makrani
HGDP00144
70.577%


Iranian
iran2
70.573%


Pakistan_Parsi
EGYPTLC5544393
70.570%


.Sein
ID001
70.567%


Makrani
HGDP00135
70.562%


Iran_Fars
IREJ-T026
70.557%


Pakistan_Parsi
EGYPTLC5544385
70.554%


Kurd_N
kurd1156
70.549%


Iranian
iran17
70.542%


Iranian_Bandari
BanII90
70.535%


Iranian_Bandari
BanII47
70.534%


.Sapporo
ID001
70.533%


Balochi
HGDP00062
70.532%


Georgian
mg47
70.530%


Iranian_Bandari
BanII55
70.530%


Iran_Fars
IREJ-T111
70.526%


Makrani
HGDP00137
70.522%


Iran_Fars
IREJ-T027
70.521%


.Kurd_F5
ID001
70.521%


Pathan
HGDP00232
70.517%


Iranian
GMII54
70.516%


Makrani
HGDP00160
70.507%


Makrani
HGDP00140
70.507%


Iranian
iran3
70.503%


Iranian
LORII51
70.503%


Makrani
HGDP00131
70.502%


.Rukha
ID001
70.502%


Kurd_N
kurd1159
70.500%


Makrani
HGDP00145
70.499%


Pakistan_Parsi
EGYPTLC5544391
70.498%


Kurd_N
kurd1160
70.495%


Pakistan_Parsi
EGYPTLC5544401
70.493%


Makrani
HGDP00148
70.487%


Iranian
LORII19
70.486%


Iran_Fars
IREJ-T009
70.475%


Iran_Zoroastrian
SH004
70.472%


Iranian
iran14
70.472%


Iranian_Bandari
BanII80
70.472%


Iranian
SHII87
70.472%


Pakistan_Parsi
EGYPTLC5544388
70.470%


.Kurd_F2
ID001
70.470%


Iran_Fars
IREJ-T006
70.466%


Iranian
SHII20
70.462%


Georgian
mg62
70.457%


Balochi
HGDP00078
70.456%


Balochi
HGDP00086
70.453%


Iran_Zoroastrian
T006
70.448%


Iranian
SHII72
70.445%


.Kurd_Ezidi
ID001
70.443%


Pathan
HGDP00264
70.442%


Iranian
LORII50
70.442%


Iranian
SHII94
70.441%


Pathan
HGDP00213
70.436%


Sindhi
HGDP00187
70.435%


Iranian
GMII20
70.433%


Iranian
LORII34
70.431%


Iranian
LORII52
70.429%


Pakistan_Parsi
EGYPTLC5544403
70.423%


Georgian
mg22
70.423%


Iranian
SHII51
70.421%


.Kurd_F1
ID001
70.418%


Iran_Zoroastrian
YZ022
70.415%


Pathan
HGDP00228
70.413%


Iranian
iran16
70.412%


.Kurd_F6
ID001
70.411%


Pakistan_Parsi
EGYPTLC5544390
70.410%


Iran_Zoroastrian
I001
70.409%


Iran_Fars
IREJ-T053
70.408%


Sindhi
HGDP00185
70.406%


.Kurd_C2
ID001
70.406%


Iran_Zoroastrian
YZ019
70.406%


Pathan
HGDP00226
70.402%


Iranian
LORII44
70.401%


.Kurd_F4
ID001
70.399%


Iranian
SHII25
70.398%


Iran_Fars
IREJ-T090
70.397%


Makrani
HGDP00136
70.397%


.Pashtun_Afg1
ID001
70.395%


Iranian
GMII7
70.392%


.Zephyrous
ID001
70.392%


.NK19191
ID001
70.390%


Pakistan_Parsi
EGYPTLC5544384
70.389%


.Kurd_C3
ID001
70.382%


Pakistan_Parsi
EGYPTLC5544394
70.382%


Georgian
mg27
70.380%


.Kurd_C7
ID001
70.379%


Pakistan_Parsi
EGYPTLC5544398
70.378%


Makrani
HGDP00141
70.377%


Iran_Fars
IREJ-T103
70.375%

Kurd
10-17-2017, 08:41 PM
cont



Iran_Zoroastrian
SH005
70.367%


Kurd_N
kurd1101
70.364%


Sindhi
HGDP00189
70.361%


Iran_Zoroastrian
T015
70.358%


Pakistan_Parsi
EGYPTLC5544399
70.358%


Pathan
HGDP00230
70.357%


Balochi
HGDP00082
70.357%


GujaratiA
NA20862
70.353%


Pakistan_Parsi
EGYPTLC5544402
70.351%


.Hanif
ID001
70.350%


Iranian
iran20
70.347%


Balochi
HGDP00072
70.346%


.Kurd_F3
ID001
70.345%


Pathan
HGDP00216
70.345%


Balochi
HGDP00054
70.341%


Baloch_IR1
ID001
70.341%


Iran_Fars
IREJ-T022
70.340%


.Jesus
ID001
70.337%


Iran_Zoroastrian
T003
70.337%


Iran_Zoroastrian
I002
70.333%


.Znertu
ID001
70.330%


Iran_Zoroastrian
SH001
70.325%


Iran_Fars
IREJ-T101
70.324%


Pathan
HGDP00254
70.324%


GujaratiA
NA20858
70.319%


GujaratiA
NA20910
70.313%


Georgian
mg49
70.313%


Iran_Zoroastrian
T007
70.312%


Kalash
HGDP00298
70.307%


.Kurd_C6
ID001
70.306%


Iran_Zoroastrian
YZ018
70.306%


Pakistan_Parsi
EGYPTLC5544387
70.305%


.Punjabi_Jatt
ID001
70.304%


Georgian
mg34
70.301%


Pathan
HGDP00241
70.296%


Balochi
HGDP00058
70.294%


.Parasar
ID001
70.292%


Iranian
iran11
70.290%


.Pashtun_Afg2
ID001
70.289%


Pakistan_Parsi
EGYPTLC5544395
70.283%


Sindhi
HGDP00205
70.282%


Makrani
HGDP00134
70.281%


.Khana
ID001
70.280%


Georgian
mg31
70.280%


Iran_Zoroastrian
T012
70.277%


Pakistan_Parsi
EGYPTLC5544389
70.277%


Pakistan_Parsi
EGYPTLC5544386
70.274%


Georgian
mg43
70.273%


Iran_Zoroastrian
T016
70.273%


GujaratiA
NA20904
70.273%


Pakistan_Parsi
EGYPTLC5544383
70.268%


Saudi
SaudiA9
70.266%


Iran_Zoroastrian
YZ035
70.262%


Sindhi
HGDP00210
70.252%


Sindhi
HGDP00197
70.251%


Pakistan_Parsi
EGYPTLC5544392
70.249%


Makrani
HGDP00133
70.246%


Iranian
LORII58
70.246%


Kalash
HGDP00315
70.244%


Iranian
SHII91
70.242%


Iran_Zoroastrian
YZ041
70.237%


Pakistan_Parsi
EGYPTLC5544404
70.235%


Pathan
HGDP00244
70.234%


Iran_Zoroastrian
T011
70.233%


Georgian
mg23
70.223%


Balochi
HGDP00088
70.223%


Pakistan_Parsi
EGYPTLC5544405
70.222%


Balochi
HGDP00094
70.219%


.Hanna
ID001
70.218%


Kalash
HGDP00319
70.213%


Pathan
HGDP00262
70.213%


Kurd_N
kurd1173
70.212%


Sindhi
HGDP00167
70.210%


Sindhi
HGDP00183
70.207%


Makrani
HGDP00153
70.198%


Iran_Fars
IREJ-T037
70.193%


Balochi
HGDP00096
70.190%


Iranian
iran19
70.189%


Iran_Zoroastrian
SH003
70.189%


Saudi
SaudiA6
70.182%


.Kurd_C8
ID001
70.181%


.Kurd_C1
ID001
70.181%


Pakistan_Parsi
EGYPTLC5544400
70.178%


Kalash
HGDP00307
70.175%


Pakistan_Parsi
EGYPTLC5544397
70.173%


Pathan
HGDP00247
70.170%


Iran_Zoroastrian
YZ037
70.168%


Iranian
GMII19
70.165%


Sindhi
HGDP00195
70.165%


.Punjabi_Gujjar
ID001
70.164%


Makrani
HGDP00154
70.164%


Makrani
HGDP00146
70.152%


.Kurd_F7
ID001
70.149%


Sindhi
HGDP00201
70.141%


GujaratiA
NA20881
70.138%


Kalash
HGDP00290
70.127%


Balochi
HGDP00064
70.123%


.Varun
ID001
70.109%


.Marathi1
ID001
70.105%


Kalash
HGDP00323
70.105%


GujaratiC
NA20883
70.098%


Sindhi
HGDP00169
70.098%


.Punjabi_Rgh
ID001
70.084%


GujaratiB
NA20854
70.075%


Kalash
HGDP00302
70.074%


Kalash
HGDP00311
70.073%


GujaratiD
NA20847
70.068%


Iran_Zoroastrian
YZ039
70.063%


.Kurd_C5
ID001
70.057%


GujaratiC
NA21116
70.055%


Albanian
ALB202
70.054%


Balochi
HGDP00068
70.054%


GujaratiC
NA20866
70.051%


Iran_Zoroastrian
T013
70.050%


GujaratiB
NA20873
70.046%


Kalash
HGDP00333
70.022%


Makrani
HGDP00157
70.009%


GujaratiD
NA20899
70.002%

Kurd
10-17-2017, 08:43 PM
cont



GujaratiD
NA20899
70.002%


Pathan
HGDP00243
69.998%


Pathan
HGDP00258
69.997%


.Kenji
ID001
69.991%


Iranian_Bandari
BanII4
69.983%


Pathan
HGDP00224
69.979%


Pathan
HGDP00248
69.972%


.Passa
ID001
69.962%


Kalash
HGDP00330
69.956%


GujaratiB
NA20898
69.955%


.McNinja
ID001
69.951%


Kalash
HGDP00313
69.947%


.Targum
ID001
69.942%


GujaratiC
NA20903
69.938%


Balochi
HGDP00066
69.933%


Saudi
SaudiA7
69.928%


GujaratiB
NA20885
69.926%


GujaratiC
NA21097
69.925%


Albanian
ALB230
69.911%


Kalash
HGDP00288
69.903%


Balochi
HGDP00090
69.902%


GujaratiD
NA20911
69.902%


Balochi
HGDP00052
69.883%


Iran_Zoroastrian
SH007
69.879%


Sindhi
HGDP00179
69.878%


Pakistan_Parsi
EGYPTLC5544382
69.875%


BedouinB
HGDP00650
69.870%


Makrani
HGDP00158
69.870%


Balochi
HGDP00074
69.865%


Albanian
ALB220
69.858%


Sindhi
HGDP00208
69.852%


Pakistan_Parsi
EGYPTLC5544396
69.851%


Sindhi
HGDP00206
69.846%


Saudi
SaudiA1
69.844%


BedouinB
HGDP00636
69.844%


Iran_Zoroastrian
YZ033
69.840%


BedouinB
HGDP00648
69.839%


Albanian
ALB213
69.838%


GujaratiB
NA20882
69.838%


.Powell
ID001
69.816%


Sindhi
HGDP00171
69.815%


Iranian_Bandari
BanII30
69.804%


GujaratiD
NA21123
69.798%


Sindhi
HGDP00192
69.792%


Kalash
HGDP00328
69.766%


Albanian
ALB191
69.764%


BedouinB
HGDP00618
69.751%


Iran_Zoroastrian
YZ030
69.750%


Sindhi
HGDP00181
69.741%


Saudi
saudi1403
69.726%


Makrani
HGDP00161
69.713%


Saudi
saudi1424
69.708%


Sindhi
HGDP00191
69.684%


Iran_Fars
IREJ-T064
69.673%


Belarusian
bel43s
69.652%


Iran_Zoroastrian
SH008
69.650%


Sardinian
HGDP01063
69.650%


Balochi
HGDP00098
69.649%


Pathan
HGDP00259
69.629%


Sardinian
HGDP00666
69.628%


Iran_Zoroastrian
YZ024
69.608%


BedouinB
HGDP00641
69.607%


Albanian
ALB212
69.597%


GujaratiD
NA21125
69.593%


Iran_Zoroastrian
YZ021
69.589%


Baloch_IR2
ID001
69.584%


BedouinB
HGDP00624
69.572%


Balochi
HGDP00092
69.543%


Belarusian
bel8s
69.541%


.Reza1
ID001
69.539%


BedouinB
HGDP00701
69.531%


BedouinB
HGDP00643
69.510%


.Sadia
ID001
69.506%


Makrani
HGDP00151
69.505%


.Tajik1
ID001
69.501%


Sardinian
HGDP01065
69.499%


Sardinian
HGDP00672
69.483%


Sardinian
HGDP01066
69.441%


Sardinian
HGDP00669
69.439%


BedouinB
HGDP00612
69.426%


Sardinian
HGDP01067
69.419%


Belarusian
bel23s
69.406%


BedouinB
HGDP00651
69.396%


Sardinian
HGDP01069
69.391%


BedouinB
HGDP00630
69.377%


Sardinian
HGDP00674
69.369%


Belarusian
bel30s
69.365%


BedouinB
HGDP00616
69.364%


Sardinian
HGDP01062
69.352%


BedouinB
HGDP00631
69.347%


Sardinian
HGDP01071
69.345%


Sardinian
HGDP00667
69.344%


Sardinian
HGDP00671
69.334%


BedouinB
HGDP00653
69.329%


Sardinian
HGDP00673
69.320%


Sardinian
HGDP01064
69.276%


Sardinian
HGDP01068
69.263%


Sardinian
HGDP00670
69.237%


Saudi
saudi1434
69.231%


Sardinian
HGDP00668
69.192%


BedouinB
HGDP00623
69.185%


Saudi
SaudiA5
69.149%


Sardinian
HGDP01070
69.124%


BedouinB
HGDP00649
68.955%


Somali
Ayodo_43S
68.134%


Somali
Ayodo_40S
68.133%


Somali
Ayodo_34S
68.129%


Somali
Ayodo_5S
68.122%


Somali
Ayodo_61S
68.073%


Somali
Ayodo_52S
67.940%


Somali
Ayodo_35S
67.901%


Somali
Ayodo_23S
67.840%


Somali
Ayodo_21S
67.749%


Somali
Ayodo_41S
67.629%

MonkeyDLuffy
10-17-2017, 10:54 PM
http://www.reactiongifs.us/wp-content/uploads/2013/08/yeah_science_breaking_bad.gif

Rukha
10-18-2017, 01:44 AM
I agree, you're right for the most part. The Arab admixture in Iranians is highly exaggerated. Heck, Iranians are more South Asian than they are Arab. I don't know why this myth is still around because it's not true, at all. Most of the Arabs who settled in Iran, settled in Iranian Central Asia, specifically Khorassan. And they likely left no trace as the Mongols sacked and razed nearly all Iranian cities in Central Asia.

There are still communities in areas like northern Afghanistan that claim Arab ancestry and whose members spoke a distinct Central Asian dialect of Arabic until recent times.

MonkeyDLuffy
10-18-2017, 02:22 AM
There are still communities in areas like northern Afghanistan that claim Arab ancestry and whose members spoke a distinct Central Asian dialect of Arabic until recent times.

The language can be brought with the introduction of Islam. For example there are some communities in Saudi Arabia which are Central Asian in origin.

pegasus
10-18-2017, 04:39 AM
I would like to add
based of Lazardis's work and even what David has shown they are definitely noteworthy differences. CHG and Iran_N are sister clades as David best describes which split off in the paleolithic, the fact CHG is best modeled with Villabruna speaks for it self, Iran_N has none of it. If it did peak in Plateau Iranians, the implications would be Eastern Anatolians would be Iran_N rich, unfortunately they are not. Even with the Sidon BA paper with a Canaanite man whose 50-55 % Iran_Chl, its mind boggling how a few are beating this decomposing horse lol.

As a personal anecdote I had the pleasure of meeting a group of Brohis in London, a community where the Iran_N component peaks in. One thing which I found striking about them was how pan South Asian they looked to the point some actually resembled South Indian IT professionals at my former work place. So it just goes to show the enormous role these Iran_N/Hotu people played in not only forming the genetic base ancestry for the vast majority of South Asians but also giving them their distinctive phenotypes.

pegasus
10-18-2017, 04:46 AM
edit..

pegasus
10-18-2017, 04:49 AM
The language can be brought with the introduction of Islam. For example there are some communities in Saudi Arabia which are Central Asian in origin.

Actually Rukha is right here, because Central Asia has Bukharan Jews who have been there since antiquity, Kabul still has like 2-3 of them lol. Afghani Arabs were a very small community and typically formed the religious class , in the same way Persians formed the religious Shia scholarly class in Northern India. In fact Ayatollah Khomeini's family descends from such a family and fled with coming of the East Indian company in Lucknow. In fact his grandfather's name is Seyyed Ahmad Musavi Hindi.

Zoran
10-18-2017, 05:59 AM
Iran_Hotu is not really the same as Iran_N, Iran_Hotu has EHG / WHG admixture contra Iran_N

Admix Results (sorted):

# Population Percent
1 West-Asian 63.7
2 Indian 10.93
3 North-East-European 7.49
4 Indo-Iranian 6.54
5 North-European-Mesolithic 4.02
6 Near_East 3.32
7 North-Amerind 3.04
8 Sub-Saharian 0.44
9 Mesoamerican 0.31
10 East-South-Asian 0.2
11 North-Siberean 0.04

Admix Results (sorted):

# Population Percent
1 West_Asia 67.62
2 NE_Europe 13.16
3 SW_Europe 7.53
4 West_Africa 6.14
5 South_Asia 5.55


Compared to Iran_N:


Admix Results (sorted):

# Population Percent
1 West-Asian 70.37
2 Indian 16.47
3 Indo-Iranian 8.48
4 Near_East 3.07
5 Sub-Saharian 1.42
6 Austronesian 0.19


Admix Results (sorted):

# Population Percent
1 West_Asia 77.14
2 South_Asia 14.58
3 SW_Asia 4.38
4 West_Africa 2.96
5 Oceania 0.71
6 East_Africa 0.23

Even in this PCA plot its evident that Iran_Hotu is somewhere in between CHG and Iran_N

https://lh3.googleusercontent.com/umE4UszQAggweHiNPfsol5GX-F1B3J8HYbkjMhZd-55z-EdEGQT2KHbKTwfr8w6ah-nrYEeM=w1920-h949-rw

pegasus
10-18-2017, 06:18 AM
Iran_Hotu is not really the same as Iran_N, Iran_Hotu has EHG / WHG admixture contra Iran_N

Admix Results (sorted):

# Population Percent
1 West-Asian 63.7
2 Indian 10.93
3 North-East-European 7.49
4 Indo-Iranian 6.54
5 North-European-Mesolithic 4.02
6 Near_East 3.32
7 North-Amerind 3.04
8 Sub-Saharian 0.44
9 Mesoamerican 0.31
10 East-South-Asian 0.2
11 North-Siberean 0.04

Admix Results (sorted):

# Population Percent
1 West_Asia 67.62
2 NE_Europe 13.16
3 SW_Europe 7.53
4 West_Africa 6.14
5 South_Asia 5.55


Compared to Iran_N:


Admix Results (sorted):

# Population Percent
1 West-Asian 70.37
2 Indian 16.47
3 Indo-Iranian 8.48
4 Near_East 3.07
5 Sub-Saharian 1.42
6 Austronesian 0.19


Admix Results (sorted):

# Population Percent
1 West_Asia 77.14
2 South_Asia 14.58
3 SW_Asia 4.38
4 West_Africa 2.96
5 Oceania 0.71
6 East_Africa 0.23

Even in this PCA plot its evident that Iran_Hotu is somewhere in between CHG and Iran_N

https://lh3.googleusercontent.com/umE4UszQAggweHiNPfsol5GX-F1B3J8HYbkjMhZd-55z-EdEGQT2KHbKTwfr8w6ah-nrYEeM=w1920-h949-rw

Iran Hotu and Iran_N are the same cline of people, their excess 13% EHG is actually excess ANE lumped and neither have Villabruna affinity ie Iran Hotu peoples became more basal over time. They are more archaic than Iran_N and are more ANE and ENA/ASE shifted compared to Iran_N whose more basal. Also its location in the Hotu Caves, near Central Asia point to the direction, where the ANE rich Paleo Siberians/Central Asians came from before mixing with basal populations in Iran, where I suspect where the elusive Basal Eurasian will be found. Using admixture calculators is not good for very ancient genomes, treemix / nMonte are the way to go.

Zoran
10-18-2017, 06:24 AM
Iran Hotu and Iran_N are the same cline of people, their excess 13% EHG is actually excess ANE lumped and neither have Villabruna affinity. They are more archaic than Iran_N and are more ANE and ENA/ASE shifted compared to Iran_N whose more basal. Also its location in the Hotu Caves, near Central Asia point to the direction, where the ANE rich Paleo Siberians/Central Asians came from before mixing with basal populations in Iran, where I suspect where the elusive Basal Eurasian will be found. Using admixture calculators is not good for very ancient genomes, treemix / nMonte are the way to go.

I agree partially but by looking at admixture we can get an idea of how things look compared to each other. Anyways, seems that Iran_N obtained more South Asian / Australoid admixture and barely shows signs of any extra ANE / EHG admixture.

pegasus
10-18-2017, 06:50 AM
I agree partially but by looking at admixture we can get an idea of how things look compared to each other. Anyways, seems that Iran_N obtained more South Asian / Australoid admixture and barely shows signs of any extra ANE / EHG admixture.

South Indians can be modeled with Iran_Hotu, their populations typically lack or have very minimal Steppe. I told you before in admixture excess ANE lumped into EHG, Iran_N are basal more and in fact of all Neolithic Farmers, Basal peaks in WC1 at 60%. ENA starts increasing as one enters S/SC Asia and jumps even more dramatically east of the Indus river . Khana put a wonderful moving visual which showed how this ENA/ASI trail which starts with Pamiris ( who have the least amount and ends with Panias where its a maximum, there is a abrupt break and u start to see Plateau Iranians and a nice cline all the way to mainland Europe because these populations lack that SE Eurasian pull which S/SC Asian have. Iran_Chl has 0 ENA, as do modern day Iranian Zoroastrians. The minor ENA amounts in modern Iranians, I think are largely brought by Central Asian Turks, but its still quite minimal.

Kurd
10-18-2017, 10:13 AM
IranN peaks in Iranic peoples. I took a little detour from work to do an allele by allele comparison (IBS) using PLINK. Broushaki had mentioned Zoroastrians and Baloch. Here are some other Iranian groups (Mazenderanis, Zoroastrians, Kurds, Parsis, SW Iranians, Balochis, and Makranis) along with a few project members thrown in. The IBS results show that Iranics top the list for allele sharing with both neolithic samples, Ganj Dareh and Wegmah Cave.

Keep in mind that the ordering will change a little once I dipolid process the samples, because pseudo-haploid ones, such as the ones published, are ill suited for IBS/IBD work.

This is consistent with the K12 Ancient Calculator ADMIXTURE calculator results. However, Gedmatch based calculators should not be relied upon for reasons I have previously discussed, the main ones include that the IranN cluster is very weak because there are only 2 samples, so what ends up happening is it turns into a predominantly S Asian cluster because of all the S Asians that gang up under it (not that different from S Asians scoring high C Asian, because they have no choice because the only other comp that describes their sub-structure is S Indian, whereas W Asians have plenty of choices in terms of W Asian and SE European comps, so they usually get pushed off to another comp). In other words, Gedmatch based calculators are highly dependent on which non-reference samples get tossed into the run.

E Pakistanis/Indians are further down the list because they don't share as many alleles with IranN as the aforementioned. This shows continuity since the neolithic in Iran. Sometime during or after the neolithic individuals related to IranN migrated from the Kurdistan area in Iran to SC/S Asia at various times. This allowed for a diffusion of the modal comp throughout the area. The reason that Baloch show elevated levels compared with E Pakistanis/Indians, is that they are relatively recent split from Kurds/W Iranians.

Any theory that contradicts this needs to 1st explain why W Iranians share such a large number of alleles with IranN.



SAMPLE
ID
Iran_N_GanjDareh


Iran_N
I1290
100.000%


Iran_n_WC1
WC1
65.823%


Balochi
HGDP00074
65.309%


Iranian
SHII72
65.282%


Makrani
HGDP00133
65.253%


Iran_Zoroastrian
YZ037
65.252%


Iranian_Bandari
BanII40
65.239%


Iranian
GMII22
65.233%


Iran_Zoroastrian
YZ020
65.167%


Iranian
SHII20
65.166%


Balochi
HGDP00052
65.162%


Kurd_N
kurd1156
65.155%


Makrani
HGDP00155
65.132%


Iranian
LORII36
65.123%


Iran_Zoroastrian
YZ039
65.118%


Iranian
LORII48
65.112%


Makrani
HGDP00135
65.111%


Iran_Zoroastrian
SH003
65.104%


Balochi
HGDP00064
65.102%


Iranian
GMII54
65.098%


Iranian
GMII19
65.093%


Iran_recent
I1955
65.090%


Iran_Fars
IREJ-T184
65.085%


Iranian
iran16
65.084%


Iranian_Bandari
BanII47
65.083%


.NK19191
ID001
65.082%


Balochi
HGDP00096
65.079%


.Znertu
ID001
65.073%


Georgian
mg49
65.071%


Iran_Zoroastrian
T006
65.070%


Iranian
iran3
65.069%


.Kurd_F6
ID001
65.058%


Makrani
HGDP00160
65.057%


Iranian
LORII51
65.050%


Kurd_N
kurd1159
65.050%


Balochi
HGDP00062
65.046%


Iranian
iran2
65.044%


Iran_Fars
IREJ-T023
65.041%


Makrani
HGDP00158
65.038%


Kurd_N
kurd1173
65.036%


Makrani
HGDP00131
65.035%


Baloch_IR2
ID001
65.031%


Iran_Zoroastrian
T016
65.028%


Iran_Zoroastrian
T013
65.021%


Iranian
GMII79
65.021%


Iran_Zoroastrian
T012
65.018%


Iranian
SHII27
65.013%


Baloch_IR1
ID001
65.010%


Iranian
GMII7
65.009%


Makrani
HGDP00154
65.002%


Iranian
GMII16
65.001%


Iranian
GMII18
64.994%


Iran_Zoroastrian
I002
64.993%


Iranian
GMII20
64.991%


.Kurd_F8
ID001
64.990%


Iran_Zoroastrian
YZ022
64.988%


Balochi
HGDP00066
64.983%


Iran_Zoroastrian
I001
64.980%


Pakistan_Parsi
EGYPTLC5544390
64.979%


Pakistan_Parsi
EGYPTLC5544384
64.977%


Iran_Zoroastrian
YZ035
64.977%


Makrani
HGDP00137
64.975%


Pathan
HGDP00264
64.974%


Makrani
HGDP00146
64.966%


Balochi
HGDP00092
64.965%


Iran_Fars
IREJ-T078
64.963%


.Mfa
ID001
64.963%


Iranian
LORII52
64.963%


Iranian
GMII29
64.961%


Iranian_Bandari
BanII90
64.961%


Georgian
mg40
64.961%


Iran_Fars
IREJ-T053
64.960%


Iran_Zoroastrian
T010
64.959%


Pakistan_Parsi
EGYPTLC5544385
64.957%


.Zephyrous
ID001
64.953%


Makrani
HGDP00157
64.953%


.Hanna
ID001
64.949%


Iranian
GMII36
64.947%


.Kurd_F7
ID001
64.946%


Makrani
HGDP00145
64.938%


Iran_Zoroastrian
T015
64.933%


Makrani
HGDP00153
64.932%


Pakistan_Parsi
EGYPTLC5544393
64.924%


Iranian
LORII44
64.923%


Iranian
iran19
64.922%


GujaratiA
NA20862
64.922%


Pakistan_Parsi
EGYPTLC5544391
64.919%


Kalash
HGDP00311
64.918%


Kalash
HGDP00328
64.917%


Iran_Fars
IREJ-T103
64.916%


Iran_Fars
IREJ-T037
64.914%


Balochi
HGDP00080
64.913%




Actually there could be an explanation since these IBS runs are based on both common and rare alleles. If IranN and CHG form a clade and their split was only a few 1000 years earlier, then if someone has substantial CHG and less IranN, they could also score high on the IranN IBS.

To drill down further, one must isolate the IranN defining mutations that have occurred after the split, and those most likely would have a low worldwide allele frequency, and use only those as a base of comparison in IBS. Iíll try to get to doing this, but I may wait till I diploid process these genomes myself, as these pseudo-haploid genomes that are floating around are ill suited for IBD/IBS.

Another thing that one do is sharing based on haplotypes, like the runs with ChromoPainter which I did for the steppe genomes towards the beginning of the thread or IBD.

A word about Iran_Hotu, it is quite low coverage, meaning that a high percentage of calls are supported by only 1 read, which could be a sequencing artifact. Also, I have not analyzed it to see the extent of post-mortem damage and how much modern human contamination it contains. Thus, it can be expected to have a high margin of error.

bmoney
10-18-2017, 03:04 PM
Iran Hotu and Iran_N are the same cline of people, their excess 13% EHG is actually excess ANE lumped and neither have Villabruna affinity ie Iran Hotu peoples became more basal over time. They are more archaic than Iran_N and are more ANE and ENA/ASE shifted compared to Iran_N whose more basal. Also its location in the Hotu Caves, near Central Asia point to the direction, where the ANE rich Paleo Siberians/Central Asians came from before mixing with basal populations in Iran, where I suspect where the elusive Basal Eurasian will be found. Using admixture calculators is not good for very ancient genomes, treemix / nMonte are the way to go.

According to this figure: http://www.nature.com/nature/journal/v536/n7617/fig_tab/nature19310_F2.html

Iran_Hotu has less Altai neanderthal and more basal eurasian component than Iran_N.

I thought they would have more Neanderthal and less Basal Eurasian as a result of more ANE

pegasus
10-18-2017, 04:34 PM
According to this figure: http://www.nature.com/nature/journal/v536/n7617/fig_tab/nature19310_F2.html

Iran_Hotu has less Altai neanderthal and more basal eurasian component than Iran_N.

I thought they would have more Neanderthal and less Basal Eurasian as a result of more ANE

WC1 has the most basal.

Zoran
10-18-2017, 11:48 PM
According to this figure: http://www.nature.com/nature/journal/v536/n7617/fig_tab/nature19310_F2.html

Iran_Hotu has less Altai neanderthal and more basal eurasian component than Iran_N.

I thought they would have more Neanderthal and less Basal Eurasian as a result of more ANE

It looks a bit fishy IMO, Iran_Hotu scoring almost 70% Basal Eurasian although its a very early split from CHG ... One member argued it didn't make sense either. I am sure Kurd could do some more testing to see whether its actually legit or not, I have my doubts.

pegasus
10-19-2017, 02:25 AM
It looks a bit fishy IMO, Iran_Hotu scoring almost 70% Basal Eurasian although its a very early split from CHG ... One member argued it didn't make sense either. I am sure Kurd could do some more testing to see whether its actually legit or not, I have my doubts.

Iran Hotu is not 70% basal its the least basal of all Iranian samples modern included, basal rises in Iran over time as new farmers from other sides of the Zagros pushed through and peaked with Iran_Chl then it goes down in modern Iranians because they have Steppe related which ancestry comes through. No need to use calculators , this summarizes it all well Hotu is the most ANE rich and least Basal of the samples, it makes sense considering Hotu's close proximity to Central Asia where ANE MA1 people came through.
https://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit#gid=1829029512

Zoran
10-19-2017, 03:22 AM
Iran Hotu is not 70% basal its the least basal of all Iranian samples modern included, basal rises in Iran over time as new farmers from other sides of the Zagros pushed through and peaked with Iran_Chl then it goes down in modern Iranians because they have Steppe related which ancestry comes through. No need to use calculators , this summarizes it all well Hotu is the most ANE rich and least Basal of the samples, it makes sense considering Hotu's close proximity to Central Asia where ANE MA1 people came through.
https://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit#gid=1829029512

Yes, it even has a little less than CHG, the reason why it increases in Iran_CHL is because they have Natufian / Levant admixture and Natufians were more Basal Eurasian shifted, I agree.

Xehanort
10-19-2017, 06:26 AM
Actually there could be an explanation since these IBS runs are based on both common and rare alleles. If IranN and CHG form a clade and their split was only a few 1000 years earlier, then if someone has substantial CHG and less IranN, they could also score high on the IranN IBS.

To drill down further, one must isolate the IranN defining mutations that have occurred after the split, and those most likely would have a low worldwide allele frequency, and use only those as a base of comparison in IBS. Iíll try to get to doing this, but I may wait till I diploid process these genomes myself, as these pseudo-haploid genomes that are floating around are ill suited for IBD/IBS.

Another thing that one do is sharing based on haplotypes, like the runs with ChromoPainter which I did for the steppe genomes towards the beginning of the thread or IBD.

A word about Iran_Hotu, it is quite low coverage, meaning that a high percentage of calls are supported by only 1 read, which could be a sequencing artifact. Also, I have not analyzed it to see the extent of post-mortem damage and how much modern human contamination it contains. Thus, it can be expected to have a high margin of error.

Thanks everyone for the replies. I appreciate it. But I had a question for Kurd. Can you explain what this chart means? Is it saying that Iranians are 65% similar to Neolithic Iranians? It's quite confusing. Also, why are Saudis almost as similar as Iranians to Neolithic Iranians? I think, I'm just reading the data wrong.

Xehanort
10-19-2017, 06:27 AM
Iran Hotu is not 70% basal its the least basal of all Iranian samples modern included, basal rises in Iran over time as new farmers from other sides of the Zagros pushed through and peaked with Iran_Chl then it goes down in modern Iranians because they have Steppe related which ancestry comes through. No need to use calculators , this summarizes it all well Hotu is the most ANE rich and least Basal of the samples, it makes sense considering Hotu's close proximity to Central Asia where ANE MA1 people came through.
https://docs.google.com/spreadsheets/d/1tFAa7oxWpcNN-OdMMjBdb4NeWKG7EkpKMzZJVW2_MME/edit#gid=1829029512

Why are you obsessed with trying to prove that Iranians have little to know affinity Neolithic Iranians? Is there a particular reason for this?

Xehanort
10-19-2017, 06:28 AM
Yes, it even has a little less than CHG, the reason why it increases in Iran_CHL is because they have Natufian / Levant admixture and Natufians were more Basal Eurasian shifted, I agree.

Good to see you active again!

Zoran
10-19-2017, 07:55 AM
Why are you obsessed with trying to prove that Iranians have little to know affinity Neolithic Iranians? Is there a particular reason for this?

Because he is partially right; modern Iranians are autosomally more similar to Chalcolithic Iranians than the Neolithic ones. The irony is that Brahui / Makrani and Baloch people are much closer to Neolithic Iranians than Iranians themselves. This is due to migrations from Levant / Anatolia that are mixed into Chalcolithic Iranians and it shifts them closer to the Middle East and slightly to Europe too, where as Neolithic Iranians are more CHG and also slightly South Asian shifted

Kurd
10-19-2017, 12:21 PM
Thanks everyone for the replies. I appreciate it. But I had a question for Kurd. Can you explain what this chart means? Is it saying that Iranians are 65% similar to Neolithic Iranians? It's quite confusing. Also, why are Saudis almost as similar as Iranians to Neolithic Iranians? I think, I'm just reading the data wrong.

Users should study some of the basics of genetics and biology to get a better idea of what I post here.

It’s all contextual so in this run using the 80,000 intersecting SNPs between the samples, modern Iranians have about 65% alleles similar to IranN out of the 80K. Modern Iranians match Iran N at about 52000/80000 positions, whereas Saudis at about 51200/80000 sites, so about 800 more matching alleles for modern Iranians.


This is artificially low because the published IranN sample is pseudo-haploid. I will eventually diploid process the sample to get a more accurate genome, if it’s coverage is at least around 3X. Once I do that then the percentage should rise to about 72% and the ordering should change some.

Obviously not all the 80000 SNPs are defining for IranN, most of them are common to all humans. If I used the 3 billion nucleotides from 1 set of the pair of homologous chromosomes as a base of comparison, then Africans and Europeans/Asians would be 99.5% similar.

If I used only the SNPs which are defining for W Asians only then the difference between modern Iranians and Saudis will increase.

Xehanort
10-19-2017, 03:46 PM
Because he is partially right; modern Iranians are autosomally more similar to Chalcolithic Iranians than the Neolithic ones. The irony is that Brahui / Makrani and Baloch people are much closer to Neolithic Iranians than Iranians themselves. This is due to migrations from Levant / Anatolia that are mixed into Chalcolithic Iranians and it shifts them closer to the Middle East and slightly to Europe too, where as Neolithic Iranians are more CHG and also slightly South Asian shifted

Okay, thanks for explaining! :)

Xehanort
10-19-2017, 03:48 PM
Users should study some of the basics of genetics and biology to get a better idea of what I post here.

It’s all contextual so in this run using the 80,000 intersecting SNPs between the samples, modern Iranians have about 65% alleles similar to IranN out of the 80K. Modern Iranians match Iran N at about 52000/80000 positions, whereas Saudis at about 51200/80000 sites, so about 800 more matching alleles for modern Iranians.


This is artificially low because the published IranN sample is pseudo-haploid. I will eventually diploid process the sample to get a more accurate genome, if it’s coverage is at least around 3X. Once I do that then the percentage should rise to about 72% and the ordering should change some.

Obviously not all the 80000 SNPs are defining for IranN, most of them are common to all humans. If I used the 3 billion nucleotides from 1 set of the pair of homologous chromosomes as a base of comparison, then Africans and Europeans/Asians would be 99.5% similar.

If I used only the SNPs which are defining for W Asians only then the difference between modern Iranians and Saudis will increase.

Thanks for the explanation. Could you please do a similar comparison for the Early Iron Age Iranian. I would like to see the results, since the Early Iron Age sample is much more representative of modern Iranians.

pegasus
10-20-2017, 01:45 PM
Why are you obsessed with trying to prove that Iranians have little to know affinity Neolithic Iranians? Is there a particular reason for this?

I don't have anything to prove when its already been proven. Ofcourse Iranians do have affinity for Iran_N relative to say Levantines but equating CHG to Iran_N is wrong for pretty much all the reasons mentioned. You really need to familiarize yourself with recent papers.
http://www.anthrogenica.com/showthread.php?10725-Ancient-DNA-from-Bronze-Age-Lebanon-(Haber-et-al-2017)

Xehanort
10-20-2017, 09:05 PM
I don't have anything to prove when its already been proven. Ofcourse Iranians do have affinity for Iran_N relative to say Levantines but equating CHG to Iran_N is wrong for pretty much all the reasons mentioned. You really need to familiarize yourself with recent papers.
http://www.anthrogenica.com/showthread.php?10725-Ancient-DNA-from-Bronze-Age-Lebanon-(Haber-et-al-2017)

Alright, I'll take a look. Thanks!

Kurd
10-23-2017, 06:21 PM
I had a little time so I decided to plot the IBS distribution for Kotias CHG from one of my IBS runs. The genome used was a diploid imputed one for better accuracy. The IBS values have been normalized. Unfortunately, I only had a couple of representatives from some of the populations in the run. May redo with more representatives or other ancients in the future.


https://i.imgur.com/AyIpaTr.png

Edit: dots = outliers
Horizontal lines inside boxes = medians
Yamnaya = Diploid samples I genotyped
Kurds= Iraqi+Iranian Kurds

Xehanort
10-25-2017, 02:19 AM
I had a little time so I decided to plot the IBS distribution for Kotias CHG from one of my IBS runs. The genome used was a diploid imputed one for better accuracy. The IBS values have been normalized. Unfortunately, I only had a couple of representatives from some of the populations in the run. May redo with more representatives or other ancients in the future.


https://i.imgur.com/AyIpaTr.png

Edit: dots = outliers
Horizontal lines inside boxes = medians
Yamnaya = Diploid samples I genotyped
Kurds= Iraqi+Iranian Kurds

Interesting, are Bandaris not really Iranian?

Dibran
10-25-2017, 06:30 PM
The numbers represent the % of autosomal sharing you have with the samples, the more red the colour is the more similar.

So if the number percentages are generally spread and lower, does this indicate more mixed recent ancestry? My mothers results seem very mixed with that similarity calculator, whereas me and my father matched the samples more commonly in Albanians/Greeks. My highest was Mycenaean at 71 percent, my father Mycenaean at 75. In most nmonte, thast drops to 60-65 percent Mycenaean like for the both of us.

Zoran
10-26-2017, 10:28 AM
So if the number percentages are generally spread and lower, does this indicate more mixed recent ancestry? My mothers results seem very mixed with that similarity calculator, whereas me and my father matched the samples more commonly in Albanians/Greeks. My highest was Mycenaean at 71 percent, my father Mycenaean at 75. In most nmonte, thast drops to 60-65 percent Mycenaean like for the both of us.

Its hard to tell, but there is always some diversity in all ethnicities, perhaps your mother might have some ancestry from another region in Albania?

Dibran
10-26-2017, 01:43 PM
Its hard to tell, but there is always some diversity in all ethnicities, perhaps your mother might have some ancestry from another region in Albania?

Perhaps. If I recall she said her paternal grandmother was from Montenegro. Perhaps some ancestry from Slavic Montenegrins. I noticed in K12 on geneplaza she gets Scandinavian Hunter Gatherers which Albanians usually do not score any of. She also gets Scandinavian and or south Slavic groups in some 4 pop mixtures.

Zoran
10-26-2017, 02:14 PM
Perhaps. If I recall she said her paternal grandmother was from Montenegro. Perhaps some ancestry from Slavic Montenegrins. I noticed in K12 on geneplaza she gets Scandinavian Hunter Gatherers which Albanians usually do not score any of. She also gets Scandinavian and or south Slavic groups in some 4 pop mixtures.

That would explain it then, Slavic admixture usually pulls you a bit North.

ztech
10-31-2017, 06:37 PM
Iran_N is fairly similar to Iran_Chalotlithic, but there is still a significant amount of Eastern hunter gatherer (via Cauacaus) influence on the Iranian plateau. There was large PIE interaction zone in the nexus between NW Iran, E. Turkey, and the Southern Caucuses, and there was gene flow in all directions. By now, it is incontrovertible given ancient DNA evidence and archaeology , that Iran Neolithics had an influence on the Steppe populations, which eventually banded out into Central Europe.

Generalissimo
10-31-2017, 10:29 PM
Iran_N is fairly similar to Iran_Chalotlithic, but there is still a significant amount of Eastern hunter gatherer (via Cauacaus) influence on the Iranian plateau. There was large PIE interaction zone in the nexus between NW Iran, E. Turkey, and the Southern Caucuses, and there was gene flow in all directions. By now, it is incontrovertible given ancient DNA evidence and archaeology , that Iran Neolithics had an influence on the Steppe populations, which eventually banded out into Central Europe.

There's no Iran_N admixture in Northern or Eastern Europe, this is certain, because it doesn't show up in haplotype analyses or uniparental markers, so Iran_N/ChL could not have migrated to the western steppe and created Yamnaya.

Zoran
11-01-2017, 09:21 AM
There's no Iran_N admixture in Northern or Eastern Europe, this is certain, because it doesn't show up in haplotype analyses or uniparental markers, so Iran_N/ChL could not have migrated to the western steppe and created Yamnaya.

Its most likely a population similar to Iran_Chl that created Yamnaya, although Iran_N and Iran_Chl are located too much to the South to have directly influenced Yamnaya

Generalissimo
11-01-2017, 09:27 AM
Its most likely a population similar to Iran_Chl that created Yamnaya, although Iran_N and Iran_Chl are located too much to the South to have directly influenced Yamnaya

Similar, but it was more likely CHG plus something from the Balkans that produced an Iran_ChL effect.

ztech
11-02-2017, 12:17 AM
There's no Iran_N admixture in Northern or Eastern Europe, this is certain, because it doesn't show up in haplotype analyses or uniparental markers, so Iran_N/ChL could not have migrated to the western steppe and created Yamnaya.

What you said is completely unfounded. A large, 2014 study by Peter A. Underhill et al., using 16,244 individuals from over 126 populations from across Eurasia, concluded that there was, "compelling evidence that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran". Also, very early R1b, including the ultra-rare R1b* (R-M343*) is exclusive to Iran. Immediately downstream, R1b1, has been found in two skeletons from prehistoric Europe: a male from the Mesolithic Samara culture (a pre-Yamna people who lived immediately north of the Caspian Sea), and a male from the early Neolithic Cardial culture, buried in about 5178Ė5066 BCE at the Els Trocs site in the Pyrenees (modern Aragon, Spain). So Iran_N certainly could have had an influence on the Steppe, and most likely did.

ztech
11-02-2017, 12:25 AM
Its most likely a population similar to Iran_Chl that created Yamnaya, although Iran_N and Iran_Chl are located too much to the South to have directly influenced Yamnaya


Oh, so they weren't real Iranians? "Too much to the south". You're the only one, who is going really out of the way. lol.

Generalissimo
11-02-2017, 12:29 AM
What you said is completely unfounded. A large, 2014 study by Peter A. Underhill et al., using 16,244 individuals from over 126 populations from across Eurasia, concluded that there was, "compelling evidence that the initial episodes of haplogroup R1a diversification likely occurred in the vicinity of present-day Iran". Also, very early R1b, including the ultra-rare R1b* (R-M343*) is exclusive to Iran. Immediately downstream, R1b1, has been found in two skeletons from prehistoric Europe: a male from the Mesolithic Samara culture (a pre-Yamna people who lived immediately north of the Caspian Sea), and a male from the early Neolithic Cardial culture, buried in about 5178–5066 BCE at the Els Trocs site in the Pyrenees (modern Aragon, Spain). So Iran_N certainly could have had an influence on the Steppe, and most likely did.

The Underhill paper is outdated. Modern-day DNA doesn't count; only ancient DNA counts. And the oldest R1a samples lack "Basal Eurasian" ancestry, so they can't be from Iran.

https://1.bp.blogspot.com/-SF74a3xkvg4/WdDa0l5addI/AAAAAAAAGH0/BM8SEreRWfMF_tpH2pfEpd20-68zOE90gCLcBGAs/s1600/R1a-M417_The_Beast.png

parasar
11-02-2017, 03:22 PM
The Underhill paper is outdated. Modern-day DNA doesn't count; only ancient DNA counts. And the oldest R1a samples lack "Basal Eurasian" ancestry, so they can't be from Iran.

https://1.bp.blogspot.com/-SF74a3xkvg4/WdDa0l5addI/AAAAAAAAGH0/BM8SEreRWfMF_tpH2pfEpd20-68zOE90gCLcBGAs/s1600/R1a-M417_The_Beast.png

Are you saying that the oldest R1a-M417 (the relevant line to nearly 100% of all extant R1a1) and the oldest *R1a-93 (Z94, on Z2124 line) have no so called "Basal Eurasian?"

*Edit: Z93

DMXX
11-02-2017, 06:12 PM
Are you saying that the oldest R1a-M417 (the relevant line to nearly 100% of all extant R1a1) and the oldest R1a-93 (Z94, on Z2124 line) have no so called "Basal Eurasian?"

It does have BE, but it's embedded within EEF.

I16561 (the Ukrainian Eneolithic sample with Y-DNA R1a-M417) looks about 65% Yamnaya, 25% EEF and 10% surplus WHG and EHG (like late Corded Ware). The Ukrainian site this sample is from also happens to be the closest geographically to the Balkans.

parasar
11-02-2017, 07:54 PM
It does have BE, but it's embedded within EEF.

I16561 (the Ukrainian Eneolithic sample with Y-DNA R1a-M417) looks about 65% Yamnaya, 25% EEF and 10% surplus WHG and EHG (like late Corded Ware). The Ukrainian site this sample is from also happens to be the closest geographically to the Balkans.

The sample is actually from the Ukraine/Russia border in eastern Ukraine.
"An Eneolithic cemetery of the Sredny Stog II culture was excavated by D. Telegin in 1955-
1957 near the village of Alexandria, Kupyansk district, Kharkov region on the left bank of the
river Oskol"
http://www.anthrogenica.com/showthread.php?10564-The-Genomic-History-of-Southeastern-Europe-Mathieson-Reich-et-al&p=288931&viewfull=1#post288931
https://en.wikipedia.org/wiki/Kupiansk

DMXX
11-02-2017, 07:55 PM
I meant relative to the other samples obtained in the study. Kharkov is closer to Chechnya than it is to the Balkans.

bmoney
11-03-2017, 12:04 AM
It does have BE, but it's embedded within EEF.

I16561 (the Ukrainian Eneolithic sample with Y-DNA R1a-M417) looks about 65% Yamnaya, 25% EEF and 10% surplus WHG and EHG (like late Corded Ware). The Ukrainian site this sample is from also happens to be the closest geographically to the Balkans.

Does this mean z93 is predominantly Yamnaya Afanisievo related as opposed to Andronovo?

DMXX
11-03-2017, 02:14 AM
Does this mean z93 is predominantly Yamnaya Afanisievo related as opposed to Andronovo?

Andronovo is an offshoot of Sintashta. Sintashta, in turn, is an offshoot of some late iteration of Yamnaya (Abashevo is my guess right now).

Abashevo is the intermediary between Corded Ware and Sintashta and predates the latter. Late CW and Sintashta both look very similar to this Ukrainian Eneolithic sample genetically (mostly Yamnaya with surplus EEF). I16561 predates both CW and Sintashta.

It's only one sample, so broad stroke inferences regarding the extent of EEF admixture in the steppes shouldn't be made just yet.

Answering your question directly now the context has been established - No, Yamnaya and Afanasievo are both too early for the Z93 mutation. Z93 is a similar age to Z282 (the European branch). If I were to guess, Z282 arose in the eastern half of Corded Ware and Z93 arose in the Abashevo culture.

parasar
11-07-2017, 05:02 PM
...

Answering your question directly now the context has been established - No, Yamnaya and Afanasievo are both too early for the Z93 mutation. Z93 is a similar age to Z282 (the European branch). If I were to guess, Z282 arose in the eastern half of Corded Ware and Z93 arose in the Abashevo culture.

Yamna and Afanasevo timelines are close to the age of both Z283 and Z93. Both Z93 and Z283 could have been born in these cultures. Corded Ware also almost overlaps Yamna and Afanasevo.
https://media.springernature.com/m685/nature-assets/nature/journal/v522/n7555/images/nature14507-f1.jpg

The Poltavka Z94 on the Z2124 line is also in the same time-frame. M780/L657 is still missing, and perhaps is related to Srubna. As to Z645 itself, I think a Baltic Corded Ware or related origin is likely.

khanabadoshi
11-29-2017, 04:53 AM
Andronovo is an offshoot of Sintashta. Sintashta, in turn, is an offshoot of some late iteration of Yamnaya (Abashevo is my guess right now).

Abashevo is the intermediary between Corded Ware and Sintashta and predates the latter. Late CW and Sintashta both look very similar to this Ukrainian Eneolithic sample genetically (mostly Yamnaya with surplus EEF). I16561 predates both CW and Sintashta.

It's only one sample, so broad stroke inferences regarding the extent of EEF admixture in the steppes shouldn't be made just yet.

Answering your question directly now the context has been established - No, Yamnaya and Afanasievo are both too early for the Z93 mutation. Z93 is a similar age to Z282 (the European branch). If I were to guess, Z282 arose in the eastern half of Corded Ware and Z93 arose in the Abashevo culture.


Yamna and Afanasevo timelines are close to the age of both Z283 and Z93. Both Z93 and Z283 could have been born in these cultures. Corded Ware also almost overlaps Yamna and Afanasevo.
https://media.springernature.com/m685/nature-assets/nature/journal/v522/n7555/images/nature14507-f1.jpg

The Poltavka Z94 on the Z2124 line is also in the same time-frame. M780/L657 is still missing, and perhaps is related to Srubna. As to Z645 itself, I think a Baltic Corded Ware or related origin is likely.


David did this run for me a while back. I'll post in order of fit:

Best run is Afanasievo (prob: 93.4%; chisq: 1.839):



left pops:
khanabadoshi
Iran_Late_Neolithic
Afanasievo
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 1.839 0.93389 0.363 0.419 0.169 0.049
0001 1 7 3.291 0.856807 0.363 0.419 0.169 0.049
0010 1 7 9.421 0.223801 0.363 0.419 0.169 0.049
0100 1 7 37.944 0 0.838 -0.000 -0.027 0.189 infeasible
1000 1 7 28.584 0 -0.000 0.694 0.367 -0.061 infeasible
0011 2 8 47.428 0 -0.000 0.694 0.367 -0.061 infeasible
0101 2 8 54.553 5.39222e-09 0.800 -0.000 0.200 0.000
0110 2 8 38.089 7.24787e-06 0.826 -0.000 0.000 0.174
1001 2 8 31.166 0.000131275 0.000 0.700 0.300 0.000
1010 2 8 81.099 2.93719e-14 0.000 0.840 -0.000 0.160
1100 2 8 317.748 0 -0.000 -0.000 1.637 -0.637 infeasible
0111 3 9 73.752 2.78554e-12 1.000 -0.000 0.000 0.000
1011 3 9 124.311 1.74756e-22 0.000 1.000 0.000 0.000
1101 3 9 442.488 0 0.000 -0.000 1.000 0.000
1110 3 9 1351.188 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.93389 - -
best pat: 0001 0.856807 chi(nested): 1.452 p-value for nested model: 0.22816
best pat: 1001 0.000131275 chi(nested): 27.874 p-value for nested model: 1.29454e-07
best pat: 0111 2.78554e-12 chi(nested): 42.586 p-value for nested model: 6.76252e-11



Very close 2nd is Poltavka (prob: 93.4%; chisq: 1.841):



left pops:
khanabadoshi
Iran_Late_Neolithic
Poltavka
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 1.841 0.933709 0.372 0.400 0.166 0.062
0001 1 7 4.358 0.737777 0.372 0.400 0.166 0.062
0010 1 7 9.324 0.230236 0.372 0.400 0.166 0.062
0100 1 7 36.816 0 0.832 -0.000 -0.017 0.185 infeasible
1000 1 7 32.425 0 0.000 0.671 0.374 -0.045 infeasible
0011 2 8 51.741 0 0.000 0.671 0.374 -0.045 infeasible
0101 2 8 53.190 9.90908e-09 0.795 -0.000 0.205 0.000
0110 2 8 36.875 1.21359e-05 0.824 -0.000 0.000 0.176
1001 2 8 33.947 4.15389e-05 0.000 0.675 0.325 0.000
1010 2 8 89.977 4.70081e-16 0.000 0.821 0.000 0.179
1100 2 8 317.504 0 0.000 -0.000 1.622 -0.622 infeasible
0111 3 9 73.510 3.10907e-12 1.000 -0.000 0.000 0.000
1011 3 9 147.711 2.62736e-27 0.000 1.000 0.000 0.000
1101 3 9 437.922 0 0.000 -0.000 1.000 0.000
1110 3 9 1344.293 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.933709 - -
best pat: 0001 0.737777 chi(nested): 2.517 p-value for nested model: 0.112659
best pat: 1001 4.15389e-05 chi(nested): 29.589 p-value for nested model: 5.34057e-08
best pat: 0111 3.10907e-12 chi(nested): 39.563 p-value for nested model: 3.17598e-10




3rd is Yamnaya Samara (prob: 84.33%; chisq: 2.718):


left pops:
khanabadoshi
Iran_Late_Neolithic
Yamnaya_Samara
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 2.718 0.843282 0.397 0.389 0.138 0.076
0001 1 7 6.552 0.476956 0.397 0.389 0.138 0.076
0010 1 7 8.137 0.320711 0.397 0.389 0.138 0.076
0100 1 7 37.466 0 0.833 -0.000 -0.027 0.195 infeasible
1000 1 7 43.280 0 0.000 0.681 0.367 -0.048 infeasible
0011 2 8 51.244 0 0.000 0.681 0.367 -0.048 infeasible
0101 2 8 55.369 3.74314e-09 0.792 -0.000 0.208 0.000
0110 2 8 37.614 8.86921e-06 0.820 -0.000 0.000 0.180
1001 2 8 44.978 3.71543e-07 0.000 0.686 0.314 0.000
1010 2 8 100.654 3.13855e-18 0.000 0.826 0.000 0.174
1100 2 8 318.009 0 0.000 -0.000 1.634 -0.634 infeasible
0111 3 9 76.332 8.62127e-13 1.000 -0.000 0.000 0.000
1011 3 9 163.071 1.70785e-30 0.000 1.000 0.000 0.000
1101 3 9 442.788 0 0.000 -0.000 1.000 0.000
1110 3 9 1355.165 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.843282 - -
best pat: 0001 0.476956 chi(nested): 3.834 p-value for nested model: 0.0502295
best pat: 0110 8.86921e-06 chi(nested): 31.062 p-value for nested model: 2.49882e-08
best pat: 0111 8.62127e-13 chi(nested): 38.717 p-value for nested model: 4.89818e-10



Distant 4th is Yamnaya Kalmykia (prob: 62.24%; chisq: 4.403):



left pops:
khanabadoshi
Iran_Late_Neolithic
Yamnaya_Kalmykia
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 4.403 0.622361 0.364 0.400 0.166 0.070
0001 1 7 7.415 0.387022 0.364 0.400 0.166 0.070
0010 1 7 11.636 0.1132 0.364 0.400 0.166 0.070
0100 1 7 37.119 0 0.835 -0.000 -0.029 0.194 infeasible
1000 1 7 32.598 0 -0.000 0.668 0.369 -0.038 infeasible
0011 2 8 59.495 0 -0.000 0.668 0.369 -0.038 infeasible
0101 2 8 54.577 5.33435e-09 0.795 -0.000 0.205 0.000
0110 2 8 37.285 1.01995e-05 0.822 -0.000 0.000 0.178
1001 2 8 33.610 4.77964e-05 0.000 0.673 0.327 0.000
1010 2 8 86.833 2.03989e-15 -0.000 0.814 0.000 0.186
1100 2 8 316.360 0 0.000 -0.000 1.632 -0.632 infeasible
0111 3 9 74.507 1.97673e-12 1.000 -0.000 0.000 0.000
1011 3 9 153.131 1.97936e-28 0.000 1.000 0.000 0.000
1101 3 9 437.655 0 0.000 -0.000 1.000 0.000
1110 3 9 1344.875 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.622361 - -
best pat: 0001 0.387022 chi(nested): 3.012 p-value for nested model: 0.0826506
best pat: 1001 4.77964e-05 chi(nested): 26.195 p-value for nested model: 3.08557e-07
best pat: 0111 1.97673e-12 chi(nested): 40.897 p-value for nested model: 1.60428e-10



Srubnaya (prob: 36.33%; chisq 4.329):



left pops:
khanabadoshi
Iran_Neolithic
Srubnaya
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
00000 0 4 4.329 0.363324 0.357 0.329 0.058 0.203 0.053
00001 1 5 6.175 0.28956 0.333 0.322 0.096 0.249 -0.000
00010 1 5 17.306 0.00395512 0.333 0.322 0.096 0.249 -0.000
00100 1 5 5.244 0.386791 0.335 0.381 0.000 0.214 0.070
01000 1 5 17.568 0.00353946 0.625 -0.000 0.229 0.101 0.045
10000 1 5 24.653 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00011 2 6 33.404 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00101 2 6 9.178 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00110 2 6 20.258 0 0.000 0.655 -0.049 0.385 0.010 infeasible
01001 2 6 18.565 0.0049644 0.599 -0.000 0.259 0.142 0.000
01010 2 6 20.998 0.00183635 0.683 -0.000 0.207 -0.000 0.110
01100 2 6 35.530 3.40188e-06 0.797 0.000 0.000 0.030 0.172
10001 2 6 24.712 0 -0.000 0.649 -0.040 0.391 0.000 infeasible
10010 2 6 115.002 0 0.000 0.814 -0.081 0.000 0.268 infeasible
10100 2 6 25.247 0 0.000 0.625 0.000 0.383 -0.008 infeasible
11000 2 6 135.170 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
00111 3 7 94.209 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
01011 3 7 34.403 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
01101 3 7 55.030 1.47052e-09 0.770 -0.000 -0.000 0.230 -0.000
01110 3 7 35.816 7.85195e-06 0.810 -0.000 0.000 0.000 0.190
10011 3 7 168.929 0 0.000 0.569 0.431 0.000 -0.000
10101 3 7 25.313 0.00066775 0.000 0.626 0.000 0.374 0.000
10110 3 7 115.955 5.32244e-22 0.000 0.765 0.000 0.000 0.235
11001 3 7 241.703 0 -0.000 -0.000 0.733 0.267 -0.000
11010 3 7 235.448 0 0.000 0.000 1.259 0.000 -0.259 infeasible
11100 3 7 379.839 0 -0.000 -0.000 0.000 1.576 -0.576 infeasible
01111 4 8 94.962 4.55409e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 272.443 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 268.299 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 493.887 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1355.366 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.363324 - -
best pat: 00100 0.386791 chi(nested): 0.915 p-value for nested model: 0.33866
best pat: 01001 0.0049644 chi(nested): 13.321 p-value for nested model: 0.000262461
best pat: 10101 0.00066775 chi(nested): 6.747 p-value for nested model: 0.0093881
best pat: 01111 4.55409e-17 chi(nested): 69.649 p-value for nested model: 7.08482e-17



Corded Ware Germany (prob: 35.9%; chisq: 4.366):



left pops:
khanabadoshi
Iran_Neolithic
Corded_Ware_Germany
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim



fixed pat wt dof chisq tail prob
00000 0 4 4.366 0.3587 0.363 0.333 0.044 0.206 0.054
00001 1 5 6.225 0.284945 0.338 0.327 0.083 0.253 -0.000
00010 1 5 17.445 0.00372893 0.338 0.327 0.083 0.253 -0.000
00100 1 5 4.834 0.436417 0.347 0.373 0.000 0.215 0.066
01000 1 5 17.353 0.00387636 0.628 -0.000 0.224 0.101 0.047
10000 1 5 25.511 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00011 2 6 33.477 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00101 2 6 8.252 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00110 2 6 19.785 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
01001 2 6 18.422 0.00526021 0.601 -0.000 0.255 0.144 0.000
01010 2 6 20.806 0.00198777 0.687 -0.000 0.201 -0.000 0.112
01100 2 6 34.422 5.57638e-06 0.797 -0.000 0.000 0.032 0.171
10001 2 6 25.526 0 0.000 0.668 -0.069 0.401 0.000 infeasible
10010 2 6 126.574 0 0.000 0.923 -0.248 0.000 0.325 infeasible
10100 2 6 26.782 0 0.000 0.626 0.000 0.397 -0.022 infeasible
11000 2 6 136.879 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
00111 3 7 92.128 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
01011 3 7 34.738 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
01101 3 7 53.681 2.71945e-09 0.770 -0.000 -0.000 0.230 -0.000
01110 3 7 34.734 1.25468e-05 0.811 -0.000 0.000 0.000 0.189
10011 3 7 185.149 0 -0.000 0.580 0.420 0.000 -0.000
10101 3 7 27.267 0.000298379 0.000 0.626 0.000 0.374 0.000
10110 3 7 130.690 4.50904e-25 0.000 0.769 0.000 0.000 0.231
11001 3 7 242.651 0 -0.000 -0.000 0.728 0.272 -0.000
11010 3 7 237.913 0 -0.000 -0.000 1.258 0.000 -0.258 infeasible
11100 3 7 379.821 0 -0.000 -0.000 0.000 1.568 -0.568 infeasible
01111 4 8 93.622 8.53662e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 257.812 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 270.320 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 492.116 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1360.989 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.3587 - -
best pat: 00100 0.436417 chi(nested): 0.468 p-value for nested model: 0.493831
best pat: 01001 0.00526021 chi(nested): 13.587 p-value for nested model: 0.000227716
best pat: 10101 0.000298379 chi(nested): 8.845 p-value for nested model: 0.00293911
best pat: 01111 8.53662e-17 chi(nested): 66.355 p-value for nested model: 3.76573e-16


Andronovo (prob: 24.6%; chisq: 5.431):



left pops:
khanabadoshi
Iran_Neolithic
Andronovo
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim



fixed pat wt dof chisq tail prob
00000 0 4 5.431 0.245824 0.371 0.316 0.064 0.201 0.048
00001 1 5 6.890 0.228966 0.343 0.317 0.095 0.246 -0.000
00010 1 5 17.656 0.00341021 0.343 0.317 0.095 0.246 -0.000
00100 1 5 6.464 0.263635 0.348 0.374 0.000 0.213 0.065
01000 1 5 17.759 0.0032646 0.625 -0.000 0.227 0.102 0.046
10000 1 5 24.076 0 0.000 0.656 -0.044 0.397 -0.009 infeasible
00011 2 6 34.465 0 0.000 0.656 -0.044 0.397 -0.009 infeasible
00101 2 6 9.506 0.147069 0.281 0.423 0.000 0.297 0.000
00110 2 6 20.530 0.0022276 0.281 0.423 0.000 0.297 0.000
01001 2 6 18.811 0.0044955 0.598 -0.000 0.258 0.145 0.000
01010 2 6 21.250 0.00165413 0.684 -0.000 0.203 -0.000 0.112
01100 2 6 35.172 3.99088e-06 0.796 0.000 0.000 0.031 0.172
10001 2 6 24.120 0 0.000 0.661 -0.052 0.391 0.000 infeasible
10010 2 6 107.010 0 0.000 0.860 -0.137 0.000 0.277 infeasible
10100 2 6 24.520 0 -0.000 0.628 0.000 0.396 -0.024 infeasible
11000 2 6 135.081 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
00111 3 7 92.572 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
01011 3 7 35.193 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
01101 3 7 54.637 1.75959e-09 0.769 -0.000 -0.000 0.231 -0.000
01110 3 7 35.475 9.10528e-06 0.810 -0.000 0.000 0.000 0.190
10011 3 7 162.394 0 -0.000 0.606 0.394 0.000 -0.000
10101 3 7 25.006 0.000756796 0.000 0.629 0.000 0.371 0.000
10110 3 7 109.270 1.30107e-20 0.000 0.773 0.000 0.000 0.227
11001 3 7 241.458 0 0.000 0.000 0.729 0.271 -0.000
11010 3 7 236.601 0 0.000 -0.000 1.258 0.000 -0.258 infeasible
11100 3 7 376.541 0 0.000 -0.000 0.000 1.574 -0.574 infeasible
01111 4 8 95.009 4.45451e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 221.266 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 268.973 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 490.465 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1357.083 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.245824 - -
best pat: 00100 0.263635 chi(nested): 1.033 p-value for nested model: 0.309513
best pat: 00101 0.147069 chi(nested): 3.042 p-value for nested model: 0.081157
best pat: 10101 0.000756796 chi(nested): 15.501 p-value for nested model: 8.24733e-05
best pat: 01111 4.45451e-17 chi(nested): 70.003 p-value for nested model: 5.92268e-17



Sintashta (prob: 8.59%; chisq: 8.16):



left pops:
khanabadoshi
Iran_Neolithic
Sintashta
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
00000 0 4 8.161 0.0858584 0.353 0.306 0.070 0.191 0.080
00001 1 5 11.871 0.036601 0.320 0.292 0.130 0.258 -0.000
00010 1 5 17.499 0.00364405 0.320 0.292 0.130 0.258 -0.000
00100 1 5 9.349 0.0959299 0.320 0.292 0.130 0.258 -0.000
01000 1 5 18.201 0.00270456 0.642 -0.000 0.213 0.074 0.070
10000 1 5 21.315 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00011 2 6 31.941 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00101 2 6 16.784 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00110 2 6 20.811 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
01001 2 6 20.468 0.00228486 0.600 -0.000 0.262 0.138 0.000
01010 2 6 19.982 0.00279037 0.686 -0.000 0.195 -0.000 0.119
01100 2 6 32.349 1.39875e-05 0.804 0.000 -0.000 0.005 0.191
10001 2 6 22.700 0.000903381 0.000 0.587 0.010 0.404 0.000
10010 2 6 93.274 0 0.000 0.824 -0.181 0.000 0.357 infeasible
10100 2 6 21.650 0.00140069 0.000 0.594 0.000 0.370 0.036
11000 2 6 132.804 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
00111 3 7 90.016 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
01011 3 7 34.974 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
01101 3 7 55.762 1.05271e-09 0.777 -0.000 -0.000 0.223 -0.000
01110 3 7 32.356 3.48911e-05 0.806 -0.000 0.000 0.000 0.194
10011 3 7 160.149 0 0.000 0.519 0.481 0.000 -0.000
10101 3 7 22.733 0.00189669 0.000 0.592 0.000 0.408 0.000
10110 3 7 96.504 5.67869e-18 0.000 0.720 0.000 0.000 0.280
11001 3 7 230.384 0 0.000 0.000 0.741 0.259 -0.000
11010 3 7 226.485 0 0.000 -0.000 1.245 0.000 -0.245 infeasible
11100 3 7 382.347 0 -0.000 -0.000 0.000 1.552 -0.552 infeasible
01111 4 8 91.905 1.908e-16 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 257.944 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 255.435 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 486.811 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1312.513 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.0858584 - -
best pat: 00100 0.0959299 chi(nested): 1.188 p-value for nested model: 0.275729
best pat: 01010 0.00279037 chi(nested): 10.633 p-value for nested model: 0.00111108
best pat: 10101 0.00189669 chi(nested): 2.752 p-value for nested model: 0.0971461
best pat: 01111 1.908e-16 chi(nested): 69.171 p-value for nested model: 9.02729e-17




khana Z282 :: Afanasievo / Poltavka > Samara > Kalmykia > Srubnaya > Corded Ware > Andronovo > Sintashta


This may help in inferring when/where Z283 and Z93 split.

parasar
11-29-2017, 05:07 AM
...



khana Z282 :: Afanasievo / Poltavka > Samara > Kalmykia > Srubnaya > Corded Ware > Andronovo > Sintashta


This may help in inferring when/where Z283 and Z93 split.

While I don't follow autosomal that much for migrations, as far as Y is concerned that looks reasonable to me.
After all the Mongolian Altai had Z93+ and the Tarim Z93-.
Also consistent with the Y Pestis analysis.
"early spread of Y. pestis: the pathogen may have entered Europe from Central Eurasia following an expansion of people from the steppe, persisted within Europe until the mid-Bronze Age, and moved back toward Central Eurasia in parallel with human populations." http://www.cell.com/current-biology/fulltext/S0960-9822(17)31328-3

bmoney
11-29-2017, 05:21 AM
David did this run for me a while back. I'll post in order of fit:

Best run is Afanasievo (prob: 93.4%; chisq: 1.839):



left pops:
khanabadoshi
Iran_Late_Neolithic
Afanasievo
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 1.839 0.93389 0.363 0.419 0.169 0.049
0001 1 7 3.291 0.856807 0.363 0.419 0.169 0.049
0010 1 7 9.421 0.223801 0.363 0.419 0.169 0.049
0100 1 7 37.944 0 0.838 -0.000 -0.027 0.189 infeasible
1000 1 7 28.584 0 -0.000 0.694 0.367 -0.061 infeasible
0011 2 8 47.428 0 -0.000 0.694 0.367 -0.061 infeasible
0101 2 8 54.553 5.39222e-09 0.800 -0.000 0.200 0.000
0110 2 8 38.089 7.24787e-06 0.826 -0.000 0.000 0.174
1001 2 8 31.166 0.000131275 0.000 0.700 0.300 0.000
1010 2 8 81.099 2.93719e-14 0.000 0.840 -0.000 0.160
1100 2 8 317.748 0 -0.000 -0.000 1.637 -0.637 infeasible
0111 3 9 73.752 2.78554e-12 1.000 -0.000 0.000 0.000
1011 3 9 124.311 1.74756e-22 0.000 1.000 0.000 0.000
1101 3 9 442.488 0 0.000 -0.000 1.000 0.000
1110 3 9 1351.188 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.93389 - -
best pat: 0001 0.856807 chi(nested): 1.452 p-value for nested model: 0.22816
best pat: 1001 0.000131275 chi(nested): 27.874 p-value for nested model: 1.29454e-07
best pat: 0111 2.78554e-12 chi(nested): 42.586 p-value for nested model: 6.76252e-11



Very close 2nd is Poltavka (prob: 93.4%; chisq: 1.841):



left pops:
khanabadoshi
Iran_Late_Neolithic
Poltavka
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 1.841 0.933709 0.372 0.400 0.166 0.062
0001 1 7 4.358 0.737777 0.372 0.400 0.166 0.062
0010 1 7 9.324 0.230236 0.372 0.400 0.166 0.062
0100 1 7 36.816 0 0.832 -0.000 -0.017 0.185 infeasible
1000 1 7 32.425 0 0.000 0.671 0.374 -0.045 infeasible
0011 2 8 51.741 0 0.000 0.671 0.374 -0.045 infeasible
0101 2 8 53.190 9.90908e-09 0.795 -0.000 0.205 0.000
0110 2 8 36.875 1.21359e-05 0.824 -0.000 0.000 0.176
1001 2 8 33.947 4.15389e-05 0.000 0.675 0.325 0.000
1010 2 8 89.977 4.70081e-16 0.000 0.821 0.000 0.179
1100 2 8 317.504 0 0.000 -0.000 1.622 -0.622 infeasible
0111 3 9 73.510 3.10907e-12 1.000 -0.000 0.000 0.000
1011 3 9 147.711 2.62736e-27 0.000 1.000 0.000 0.000
1101 3 9 437.922 0 0.000 -0.000 1.000 0.000
1110 3 9 1344.293 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.933709 - -
best pat: 0001 0.737777 chi(nested): 2.517 p-value for nested model: 0.112659
best pat: 1001 4.15389e-05 chi(nested): 29.589 p-value for nested model: 5.34057e-08
best pat: 0111 3.10907e-12 chi(nested): 39.563 p-value for nested model: 3.17598e-10




3rd is Yamnaya Samara (prob: 84.33%; chisq: 2.718):


left pops:
khanabadoshi
Iran_Late_Neolithic
Yamnaya_Samara
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 2.718 0.843282 0.397 0.389 0.138 0.076
0001 1 7 6.552 0.476956 0.397 0.389 0.138 0.076
0010 1 7 8.137 0.320711 0.397 0.389 0.138 0.076
0100 1 7 37.466 0 0.833 -0.000 -0.027 0.195 infeasible
1000 1 7 43.280 0 0.000 0.681 0.367 -0.048 infeasible
0011 2 8 51.244 0 0.000 0.681 0.367 -0.048 infeasible
0101 2 8 55.369 3.74314e-09 0.792 -0.000 0.208 0.000
0110 2 8 37.614 8.86921e-06 0.820 -0.000 0.000 0.180
1001 2 8 44.978 3.71543e-07 0.000 0.686 0.314 0.000
1010 2 8 100.654 3.13855e-18 0.000 0.826 0.000 0.174
1100 2 8 318.009 0 0.000 -0.000 1.634 -0.634 infeasible
0111 3 9 76.332 8.62127e-13 1.000 -0.000 0.000 0.000
1011 3 9 163.071 1.70785e-30 0.000 1.000 0.000 0.000
1101 3 9 442.788 0 0.000 -0.000 1.000 0.000
1110 3 9 1355.165 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.843282 - -
best pat: 0001 0.476956 chi(nested): 3.834 p-value for nested model: 0.0502295
best pat: 0110 8.86921e-06 chi(nested): 31.062 p-value for nested model: 2.49882e-08
best pat: 0111 8.62127e-13 chi(nested): 38.717 p-value for nested model: 4.89818e-10



Distant 4th is Yamnaya Kalmykia (prob: 62.24%; chisq: 4.403):



left pops:
khanabadoshi
Iran_Late_Neolithic
Yamnaya_Kalmykia
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 4.403 0.622361 0.364 0.400 0.166 0.070
0001 1 7 7.415 0.387022 0.364 0.400 0.166 0.070
0010 1 7 11.636 0.1132 0.364 0.400 0.166 0.070
0100 1 7 37.119 0 0.835 -0.000 -0.029 0.194 infeasible
1000 1 7 32.598 0 -0.000 0.668 0.369 -0.038 infeasible
0011 2 8 59.495 0 -0.000 0.668 0.369 -0.038 infeasible
0101 2 8 54.577 5.33435e-09 0.795 -0.000 0.205 0.000
0110 2 8 37.285 1.01995e-05 0.822 -0.000 0.000 0.178
1001 2 8 33.610 4.77964e-05 0.000 0.673 0.327 0.000
1010 2 8 86.833 2.03989e-15 -0.000 0.814 0.000 0.186
1100 2 8 316.360 0 0.000 -0.000 1.632 -0.632 infeasible
0111 3 9 74.507 1.97673e-12 1.000 -0.000 0.000 0.000
1011 3 9 153.131 1.97936e-28 0.000 1.000 0.000 0.000
1101 3 9 437.655 0 0.000 -0.000 1.000 0.000
1110 3 9 1344.875 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.622361 - -
best pat: 0001 0.387022 chi(nested): 3.012 p-value for nested model: 0.0826506
best pat: 1001 4.77964e-05 chi(nested): 26.195 p-value for nested model: 3.08557e-07
best pat: 0111 1.97673e-12 chi(nested): 40.897 p-value for nested model: 1.60428e-10



Srubnaya (prob: 36.33%; chisq 4.329):



left pops:
khanabadoshi
Iran_Neolithic
Srubnaya
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
00000 0 4 4.329 0.363324 0.357 0.329 0.058 0.203 0.053
00001 1 5 6.175 0.28956 0.333 0.322 0.096 0.249 -0.000
00010 1 5 17.306 0.00395512 0.333 0.322 0.096 0.249 -0.000
00100 1 5 5.244 0.386791 0.335 0.381 0.000 0.214 0.070
01000 1 5 17.568 0.00353946 0.625 -0.000 0.229 0.101 0.045
10000 1 5 24.653 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00011 2 6 33.404 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00101 2 6 9.178 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00110 2 6 20.258 0 0.000 0.655 -0.049 0.385 0.010 infeasible
01001 2 6 18.565 0.0049644 0.599 -0.000 0.259 0.142 0.000
01010 2 6 20.998 0.00183635 0.683 -0.000 0.207 -0.000 0.110
01100 2 6 35.530 3.40188e-06 0.797 0.000 0.000 0.030 0.172
10001 2 6 24.712 0 -0.000 0.649 -0.040 0.391 0.000 infeasible
10010 2 6 115.002 0 0.000 0.814 -0.081 0.000 0.268 infeasible
10100 2 6 25.247 0 0.000 0.625 0.000 0.383 -0.008 infeasible
11000 2 6 135.170 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
00111 3 7 94.209 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
01011 3 7 34.403 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
01101 3 7 55.030 1.47052e-09 0.770 -0.000 -0.000 0.230 -0.000
01110 3 7 35.816 7.85195e-06 0.810 -0.000 0.000 0.000 0.190
10011 3 7 168.929 0 0.000 0.569 0.431 0.000 -0.000
10101 3 7 25.313 0.00066775 0.000 0.626 0.000 0.374 0.000
10110 3 7 115.955 5.32244e-22 0.000 0.765 0.000 0.000 0.235
11001 3 7 241.703 0 -0.000 -0.000 0.733 0.267 -0.000
11010 3 7 235.448 0 0.000 0.000 1.259 0.000 -0.259 infeasible
11100 3 7 379.839 0 -0.000 -0.000 0.000 1.576 -0.576 infeasible
01111 4 8 94.962 4.55409e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 272.443 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 268.299 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 493.887 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1355.366 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.363324 - -
best pat: 00100 0.386791 chi(nested): 0.915 p-value for nested model: 0.33866
best pat: 01001 0.0049644 chi(nested): 13.321 p-value for nested model: 0.000262461
best pat: 10101 0.00066775 chi(nested): 6.747 p-value for nested model: 0.0093881
best pat: 01111 4.55409e-17 chi(nested): 69.649 p-value for nested model: 7.08482e-17



Corded Ware Germany (prob: 35.9%; chisq: 4.366):



left pops:
khanabadoshi
Iran_Neolithic
Corded_Ware_Germany
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim



fixed pat wt dof chisq tail prob
00000 0 4 4.366 0.3587 0.363 0.333 0.044 0.206 0.054
00001 1 5 6.225 0.284945 0.338 0.327 0.083 0.253 -0.000
00010 1 5 17.445 0.00372893 0.338 0.327 0.083 0.253 -0.000
00100 1 5 4.834 0.436417 0.347 0.373 0.000 0.215 0.066
01000 1 5 17.353 0.00387636 0.628 -0.000 0.224 0.101 0.047
10000 1 5 25.511 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00011 2 6 33.477 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00101 2 6 8.252 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00110 2 6 19.785 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
01001 2 6 18.422 0.00526021 0.601 -0.000 0.255 0.144 0.000
01010 2 6 20.806 0.00198777 0.687 -0.000 0.201 -0.000 0.112
01100 2 6 34.422 5.57638e-06 0.797 -0.000 0.000 0.032 0.171
10001 2 6 25.526 0 0.000 0.668 -0.069 0.401 0.000 infeasible
10010 2 6 126.574 0 0.000 0.923 -0.248 0.000 0.325 infeasible
10100 2 6 26.782 0 0.000 0.626 0.000 0.397 -0.022 infeasible
11000 2 6 136.879 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
00111 3 7 92.128 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
01011 3 7 34.738 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
01101 3 7 53.681 2.71945e-09 0.770 -0.000 -0.000 0.230 -0.000
01110 3 7 34.734 1.25468e-05 0.811 -0.000 0.000 0.000 0.189
10011 3 7 185.149 0 -0.000 0.580 0.420 0.000 -0.000
10101 3 7 27.267 0.000298379 0.000 0.626 0.000 0.374 0.000
10110 3 7 130.690 4.50904e-25 0.000 0.769 0.000 0.000 0.231
11001 3 7 242.651 0 -0.000 -0.000 0.728 0.272 -0.000
11010 3 7 237.913 0 -0.000 -0.000 1.258 0.000 -0.258 infeasible
11100 3 7 379.821 0 -0.000 -0.000 0.000 1.568 -0.568 infeasible
01111 4 8 93.622 8.53662e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 257.812 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 270.320 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 492.116 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1360.989 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.3587 - -
best pat: 00100 0.436417 chi(nested): 0.468 p-value for nested model: 0.493831
best pat: 01001 0.00526021 chi(nested): 13.587 p-value for nested model: 0.000227716
best pat: 10101 0.000298379 chi(nested): 8.845 p-value for nested model: 0.00293911
best pat: 01111 8.53662e-17 chi(nested): 66.355 p-value for nested model: 3.76573e-16


Andronovo (prob: 24.6%; chisq: 5.431):



left pops:
khanabadoshi
Iran_Neolithic
Andronovo
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim



fixed pat wt dof chisq tail prob
00000 0 4 5.431 0.245824 0.371 0.316 0.064 0.201 0.048
00001 1 5 6.890 0.228966 0.343 0.317 0.095 0.246 -0.000
00010 1 5 17.656 0.00341021 0.343 0.317 0.095 0.246 -0.000
00100 1 5 6.464 0.263635 0.348 0.374 0.000 0.213 0.065
01000 1 5 17.759 0.0032646 0.625 -0.000 0.227 0.102 0.046
10000 1 5 24.076 0 0.000 0.656 -0.044 0.397 -0.009 infeasible
00011 2 6 34.465 0 0.000 0.656 -0.044 0.397 -0.009 infeasible
00101 2 6 9.506 0.147069 0.281 0.423 0.000 0.297 0.000
00110 2 6 20.530 0.0022276 0.281 0.423 0.000 0.297 0.000
01001 2 6 18.811 0.0044955 0.598 -0.000 0.258 0.145 0.000
01010 2 6 21.250 0.00165413 0.684 -0.000 0.203 -0.000 0.112
01100 2 6 35.172 3.99088e-06 0.796 0.000 0.000 0.031 0.172
10001 2 6 24.120 0 0.000 0.661 -0.052 0.391 0.000 infeasible
10010 2 6 107.010 0 0.000 0.860 -0.137 0.000 0.277 infeasible
10100 2 6 24.520 0 -0.000 0.628 0.000 0.396 -0.024 infeasible
11000 2 6 135.081 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
00111 3 7 92.572 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
01011 3 7 35.193 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
01101 3 7 54.637 1.75959e-09 0.769 -0.000 -0.000 0.231 -0.000
01110 3 7 35.475 9.10528e-06 0.810 -0.000 0.000 0.000 0.190
10011 3 7 162.394 0 -0.000 0.606 0.394 0.000 -0.000
10101 3 7 25.006 0.000756796 0.000 0.629 0.000 0.371 0.000
10110 3 7 109.270 1.30107e-20 0.000 0.773 0.000 0.000 0.227
11001 3 7 241.458 0 0.000 0.000 0.729 0.271 -0.000
11010 3 7 236.601 0 0.000 -0.000 1.258 0.000 -0.258 infeasible
11100 3 7 376.541 0 0.000 -0.000 0.000 1.574 -0.574 infeasible
01111 4 8 95.009 4.45451e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 221.266 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 268.973 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 490.465 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1357.083 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.245824 - -
best pat: 00100 0.263635 chi(nested): 1.033 p-value for nested model: 0.309513
best pat: 00101 0.147069 chi(nested): 3.042 p-value for nested model: 0.081157
best pat: 10101 0.000756796 chi(nested): 15.501 p-value for nested model: 8.24733e-05
best pat: 01111 4.45451e-17 chi(nested): 70.003 p-value for nested model: 5.92268e-17



Sintashta (prob: 8.59%; chisq: 8.16):



left pops:
khanabadoshi
Iran_Neolithic
Sintashta
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
00000 0 4 8.161 0.0858584 0.353 0.306 0.070 0.191 0.080
00001 1 5 11.871 0.036601 0.320 0.292 0.130 0.258 -0.000
00010 1 5 17.499 0.00364405 0.320 0.292 0.130 0.258 -0.000
00100 1 5 9.349 0.0959299 0.320 0.292 0.130 0.258 -0.000
01000 1 5 18.201 0.00270456 0.642 -0.000 0.213 0.074 0.070
10000 1 5 21.315 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00011 2 6 31.941 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00101 2 6 16.784 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00110 2 6 20.811 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
01001 2 6 20.468 0.00228486 0.600 -0.000 0.262 0.138 0.000
01010 2 6 19.982 0.00279037 0.686 -0.000 0.195 -0.000 0.119
01100 2 6 32.349 1.39875e-05 0.804 0.000 -0.000 0.005 0.191
10001 2 6 22.700 0.000903381 0.000 0.587 0.010 0.404 0.000
10010 2 6 93.274 0 0.000 0.824 -0.181 0.000 0.357 infeasible
10100 2 6 21.650 0.00140069 0.000 0.594 0.000 0.370 0.036
11000 2 6 132.804 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
00111 3 7 90.016 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
01011 3 7 34.974 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
01101 3 7 55.762 1.05271e-09 0.777 -0.000 -0.000 0.223 -0.000
01110 3 7 32.356 3.48911e-05 0.806 -0.000 0.000 0.000 0.194
10011 3 7 160.149 0 0.000 0.519 0.481 0.000 -0.000
10101 3 7 22.733 0.00189669 0.000 0.592 0.000 0.408 0.000
10110 3 7 96.504 5.67869e-18 0.000 0.720 0.000 0.000 0.280
11001 3 7 230.384 0 0.000 0.000 0.741 0.259 -0.000
11010 3 7 226.485 0 0.000 -0.000 1.245 0.000 -0.245 infeasible
11100 3 7 382.347 0 -0.000 -0.000 0.000 1.552 -0.552 infeasible
01111 4 8 91.905 1.908e-16 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 257.944 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 255.435 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 486.811 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1312.513 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.0858584 - -
best pat: 00100 0.0959299 chi(nested): 1.188 p-value for nested model: 0.275729
best pat: 01010 0.00279037 chi(nested): 10.633 p-value for nested model: 0.00111108
best pat: 10101 0.00189669 chi(nested): 2.752 p-value for nested model: 0.0971461
best pat: 01111 1.908e-16 chi(nested): 69.171 p-value for nested model: 9.02729e-17




khana Z282 :: Afanasievo / Poltavka > Samara > Kalmykia > Srubnaya > Corded Ware > Andronovo > Sintashta


This may help in inferring when/where Z283 and Z93 split.

So Z93 rose in the Afanisievo?

khanabadoshi
11-30-2017, 04:59 AM
So Z93 rose in the Afanisievo?

Dunno, I'm not Z93, I'm Z282; which is why we did these runs to see if anything stood out.

murtazasayeed
11-30-2017, 01:07 PM
Ancient Iranians of Khorassan east of Arya can be found in Balkh, in modern day Afghanistan. Those people speak the old dialect of Farsi, and is the home of Zaraostrianism and Rumi. I am also from there lol. Balkh e Bastaan...

Xehanort
12-11-2017, 09:54 PM
Ancient Iranians of Khorassan east of Arya can be found in Balkh, in modern day Afghanistan. Those people speak the old dialect of Farsi, and is the home of Zaraostrianism and Rumi. I am also from there lol. Balkh e Bastaan...

Yeah, I saw your Youtube video a while back. Your Y-DNA suggests a Greek origin, btw.

Xehanort
12-11-2017, 09:56 PM
David did this run for me a while back. I'll post in order of fit:

Best run is Afanasievo (prob: 93.4%; chisq: 1.839):



left pops:
khanabadoshi
Iran_Late_Neolithic
Afanasievo
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 1.839 0.93389 0.363 0.419 0.169 0.049
0001 1 7 3.291 0.856807 0.363 0.419 0.169 0.049
0010 1 7 9.421 0.223801 0.363 0.419 0.169 0.049
0100 1 7 37.944 0 0.838 -0.000 -0.027 0.189 infeasible
1000 1 7 28.584 0 -0.000 0.694 0.367 -0.061 infeasible
0011 2 8 47.428 0 -0.000 0.694 0.367 -0.061 infeasible
0101 2 8 54.553 5.39222e-09 0.800 -0.000 0.200 0.000
0110 2 8 38.089 7.24787e-06 0.826 -0.000 0.000 0.174
1001 2 8 31.166 0.000131275 0.000 0.700 0.300 0.000
1010 2 8 81.099 2.93719e-14 0.000 0.840 -0.000 0.160
1100 2 8 317.748 0 -0.000 -0.000 1.637 -0.637 infeasible
0111 3 9 73.752 2.78554e-12 1.000 -0.000 0.000 0.000
1011 3 9 124.311 1.74756e-22 0.000 1.000 0.000 0.000
1101 3 9 442.488 0 0.000 -0.000 1.000 0.000
1110 3 9 1351.188 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.93389 - -
best pat: 0001 0.856807 chi(nested): 1.452 p-value for nested model: 0.22816
best pat: 1001 0.000131275 chi(nested): 27.874 p-value for nested model: 1.29454e-07
best pat: 0111 2.78554e-12 chi(nested): 42.586 p-value for nested model: 6.76252e-11



Very close 2nd is Poltavka (prob: 93.4%; chisq: 1.841):



left pops:
khanabadoshi
Iran_Late_Neolithic
Poltavka
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 1.841 0.933709 0.372 0.400 0.166 0.062
0001 1 7 4.358 0.737777 0.372 0.400 0.166 0.062
0010 1 7 9.324 0.230236 0.372 0.400 0.166 0.062
0100 1 7 36.816 0 0.832 -0.000 -0.017 0.185 infeasible
1000 1 7 32.425 0 0.000 0.671 0.374 -0.045 infeasible
0011 2 8 51.741 0 0.000 0.671 0.374 -0.045 infeasible
0101 2 8 53.190 9.90908e-09 0.795 -0.000 0.205 0.000
0110 2 8 36.875 1.21359e-05 0.824 -0.000 0.000 0.176
1001 2 8 33.947 4.15389e-05 0.000 0.675 0.325 0.000
1010 2 8 89.977 4.70081e-16 0.000 0.821 0.000 0.179
1100 2 8 317.504 0 0.000 -0.000 1.622 -0.622 infeasible
0111 3 9 73.510 3.10907e-12 1.000 -0.000 0.000 0.000
1011 3 9 147.711 2.62736e-27 0.000 1.000 0.000 0.000
1101 3 9 437.922 0 0.000 -0.000 1.000 0.000
1110 3 9 1344.293 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.933709 - -
best pat: 0001 0.737777 chi(nested): 2.517 p-value for nested model: 0.112659
best pat: 1001 4.15389e-05 chi(nested): 29.589 p-value for nested model: 5.34057e-08
best pat: 0111 3.10907e-12 chi(nested): 39.563 p-value for nested model: 3.17598e-10




3rd is Yamnaya Samara (prob: 84.33%; chisq: 2.718):


left pops:
khanabadoshi
Iran_Late_Neolithic
Yamnaya_Samara
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 2.718 0.843282 0.397 0.389 0.138 0.076
0001 1 7 6.552 0.476956 0.397 0.389 0.138 0.076
0010 1 7 8.137 0.320711 0.397 0.389 0.138 0.076
0100 1 7 37.466 0 0.833 -0.000 -0.027 0.195 infeasible
1000 1 7 43.280 0 0.000 0.681 0.367 -0.048 infeasible
0011 2 8 51.244 0 0.000 0.681 0.367 -0.048 infeasible
0101 2 8 55.369 3.74314e-09 0.792 -0.000 0.208 0.000
0110 2 8 37.614 8.86921e-06 0.820 -0.000 0.000 0.180
1001 2 8 44.978 3.71543e-07 0.000 0.686 0.314 0.000
1010 2 8 100.654 3.13855e-18 0.000 0.826 0.000 0.174
1100 2 8 318.009 0 0.000 -0.000 1.634 -0.634 infeasible
0111 3 9 76.332 8.62127e-13 1.000 -0.000 0.000 0.000
1011 3 9 163.071 1.70785e-30 0.000 1.000 0.000 0.000
1101 3 9 442.788 0 0.000 -0.000 1.000 0.000
1110 3 9 1355.165 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.843282 - -
best pat: 0001 0.476956 chi(nested): 3.834 p-value for nested model: 0.0502295
best pat: 0110 8.86921e-06 chi(nested): 31.062 p-value for nested model: 2.49882e-08
best pat: 0111 8.62127e-13 chi(nested): 38.717 p-value for nested model: 4.89818e-10



Distant 4th is Yamnaya Kalmykia (prob: 62.24%; chisq: 4.403):



left pops:
khanabadoshi
Iran_Late_Neolithic
Yamnaya_Kalmykia
Andamanese_Onge
Han

right pops:
AG3-MA1
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
0000 0 6 4.403 0.622361 0.364 0.400 0.166 0.070
0001 1 7 7.415 0.387022 0.364 0.400 0.166 0.070
0010 1 7 11.636 0.1132 0.364 0.400 0.166 0.070
0100 1 7 37.119 0 0.835 -0.000 -0.029 0.194 infeasible
1000 1 7 32.598 0 -0.000 0.668 0.369 -0.038 infeasible
0011 2 8 59.495 0 -0.000 0.668 0.369 -0.038 infeasible
0101 2 8 54.577 5.33435e-09 0.795 -0.000 0.205 0.000
0110 2 8 37.285 1.01995e-05 0.822 -0.000 0.000 0.178
1001 2 8 33.610 4.77964e-05 0.000 0.673 0.327 0.000
1010 2 8 86.833 2.03989e-15 -0.000 0.814 0.000 0.186
1100 2 8 316.360 0 0.000 -0.000 1.632 -0.632 infeasible
0111 3 9 74.507 1.97673e-12 1.000 -0.000 0.000 0.000
1011 3 9 153.131 1.97936e-28 0.000 1.000 0.000 0.000
1101 3 9 437.655 0 0.000 -0.000 1.000 0.000
1110 3 9 1344.875 0 0.000 -0.000 0.000 1.000
best pat: 0000 0.622361 - -
best pat: 0001 0.387022 chi(nested): 3.012 p-value for nested model: 0.0826506
best pat: 1001 4.77964e-05 chi(nested): 26.195 p-value for nested model: 3.08557e-07
best pat: 0111 1.97673e-12 chi(nested): 40.897 p-value for nested model: 1.60428e-10



Srubnaya (prob: 36.33%; chisq 4.329):



left pops:
khanabadoshi
Iran_Neolithic
Srubnaya
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
00000 0 4 4.329 0.363324 0.357 0.329 0.058 0.203 0.053
00001 1 5 6.175 0.28956 0.333 0.322 0.096 0.249 -0.000
00010 1 5 17.306 0.00395512 0.333 0.322 0.096 0.249 -0.000
00100 1 5 5.244 0.386791 0.335 0.381 0.000 0.214 0.070
01000 1 5 17.568 0.00353946 0.625 -0.000 0.229 0.101 0.045
10000 1 5 24.653 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00011 2 6 33.404 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00101 2 6 9.178 0 0.000 0.655 -0.049 0.385 0.010 infeasible
00110 2 6 20.258 0 0.000 0.655 -0.049 0.385 0.010 infeasible
01001 2 6 18.565 0.0049644 0.599 -0.000 0.259 0.142 0.000
01010 2 6 20.998 0.00183635 0.683 -0.000 0.207 -0.000 0.110
01100 2 6 35.530 3.40188e-06 0.797 0.000 0.000 0.030 0.172
10001 2 6 24.712 0 -0.000 0.649 -0.040 0.391 0.000 infeasible
10010 2 6 115.002 0 0.000 0.814 -0.081 0.000 0.268 infeasible
10100 2 6 25.247 0 0.000 0.625 0.000 0.383 -0.008 infeasible
11000 2 6 135.170 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
00111 3 7 94.209 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
01011 3 7 34.403 0 0.000 -0.000 0.813 0.641 -0.454 infeasible
01101 3 7 55.030 1.47052e-09 0.770 -0.000 -0.000 0.230 -0.000
01110 3 7 35.816 7.85195e-06 0.810 -0.000 0.000 0.000 0.190
10011 3 7 168.929 0 0.000 0.569 0.431 0.000 -0.000
10101 3 7 25.313 0.00066775 0.000 0.626 0.000 0.374 0.000
10110 3 7 115.955 5.32244e-22 0.000 0.765 0.000 0.000 0.235
11001 3 7 241.703 0 -0.000 -0.000 0.733 0.267 -0.000
11010 3 7 235.448 0 0.000 0.000 1.259 0.000 -0.259 infeasible
11100 3 7 379.839 0 -0.000 -0.000 0.000 1.576 -0.576 infeasible
01111 4 8 94.962 4.55409e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 272.443 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 268.299 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 493.887 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1355.366 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.363324 - -
best pat: 00100 0.386791 chi(nested): 0.915 p-value for nested model: 0.33866
best pat: 01001 0.0049644 chi(nested): 13.321 p-value for nested model: 0.000262461
best pat: 10101 0.00066775 chi(nested): 6.747 p-value for nested model: 0.0093881
best pat: 01111 4.55409e-17 chi(nested): 69.649 p-value for nested model: 7.08482e-17



Corded Ware Germany (prob: 35.9%; chisq: 4.366):



left pops:
khanabadoshi
Iran_Neolithic
Corded_Ware_Germany
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim



fixed pat wt dof chisq tail prob
00000 0 4 4.366 0.3587 0.363 0.333 0.044 0.206 0.054
00001 1 5 6.225 0.284945 0.338 0.327 0.083 0.253 -0.000
00010 1 5 17.445 0.00372893 0.338 0.327 0.083 0.253 -0.000
00100 1 5 4.834 0.436417 0.347 0.373 0.000 0.215 0.066
01000 1 5 17.353 0.00387636 0.628 -0.000 0.224 0.101 0.047
10000 1 5 25.511 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00011 2 6 33.477 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00101 2 6 8.252 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
00110 2 6 19.785 0 -0.000 0.671 -0.074 0.398 0.005 infeasible
01001 2 6 18.422 0.00526021 0.601 -0.000 0.255 0.144 0.000
01010 2 6 20.806 0.00198777 0.687 -0.000 0.201 -0.000 0.112
01100 2 6 34.422 5.57638e-06 0.797 -0.000 0.000 0.032 0.171
10001 2 6 25.526 0 0.000 0.668 -0.069 0.401 0.000 infeasible
10010 2 6 126.574 0 0.000 0.923 -0.248 0.000 0.325 infeasible
10100 2 6 26.782 0 0.000 0.626 0.000 0.397 -0.022 infeasible
11000 2 6 136.879 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
00111 3 7 92.128 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
01011 3 7 34.738 0 0.000 -0.000 0.808 0.643 -0.451 infeasible
01101 3 7 53.681 2.71945e-09 0.770 -0.000 -0.000 0.230 -0.000
01110 3 7 34.734 1.25468e-05 0.811 -0.000 0.000 0.000 0.189
10011 3 7 185.149 0 -0.000 0.580 0.420 0.000 -0.000
10101 3 7 27.267 0.000298379 0.000 0.626 0.000 0.374 0.000
10110 3 7 130.690 4.50904e-25 0.000 0.769 0.000 0.000 0.231
11001 3 7 242.651 0 -0.000 -0.000 0.728 0.272 -0.000
11010 3 7 237.913 0 -0.000 -0.000 1.258 0.000 -0.258 infeasible
11100 3 7 379.821 0 -0.000 -0.000 0.000 1.568 -0.568 infeasible
01111 4 8 93.622 8.53662e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 257.812 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 270.320 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 492.116 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1360.989 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.3587 - -
best pat: 00100 0.436417 chi(nested): 0.468 p-value for nested model: 0.493831
best pat: 01001 0.00526021 chi(nested): 13.587 p-value for nested model: 0.000227716
best pat: 10101 0.000298379 chi(nested): 8.845 p-value for nested model: 0.00293911
best pat: 01111 8.53662e-17 chi(nested): 66.355 p-value for nested model: 3.76573e-16


Andronovo (prob: 24.6%; chisq: 5.431):



left pops:
khanabadoshi
Iran_Neolithic
Andronovo
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim



fixed pat wt dof chisq tail prob
00000 0 4 5.431 0.245824 0.371 0.316 0.064 0.201 0.048
00001 1 5 6.890 0.228966 0.343 0.317 0.095 0.246 -0.000
00010 1 5 17.656 0.00341021 0.343 0.317 0.095 0.246 -0.000
00100 1 5 6.464 0.263635 0.348 0.374 0.000 0.213 0.065
01000 1 5 17.759 0.0032646 0.625 -0.000 0.227 0.102 0.046
10000 1 5 24.076 0 0.000 0.656 -0.044 0.397 -0.009 infeasible
00011 2 6 34.465 0 0.000 0.656 -0.044 0.397 -0.009 infeasible
00101 2 6 9.506 0.147069 0.281 0.423 0.000 0.297 0.000
00110 2 6 20.530 0.0022276 0.281 0.423 0.000 0.297 0.000
01001 2 6 18.811 0.0044955 0.598 -0.000 0.258 0.145 0.000
01010 2 6 21.250 0.00165413 0.684 -0.000 0.203 -0.000 0.112
01100 2 6 35.172 3.99088e-06 0.796 0.000 0.000 0.031 0.172
10001 2 6 24.120 0 0.000 0.661 -0.052 0.391 0.000 infeasible
10010 2 6 107.010 0 0.000 0.860 -0.137 0.000 0.277 infeasible
10100 2 6 24.520 0 -0.000 0.628 0.000 0.396 -0.024 infeasible
11000 2 6 135.081 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
00111 3 7 92.572 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
01011 3 7 35.193 0 -0.000 -0.000 0.808 0.646 -0.454 infeasible
01101 3 7 54.637 1.75959e-09 0.769 -0.000 -0.000 0.231 -0.000
01110 3 7 35.475 9.10528e-06 0.810 -0.000 0.000 0.000 0.190
10011 3 7 162.394 0 -0.000 0.606 0.394 0.000 -0.000
10101 3 7 25.006 0.000756796 0.000 0.629 0.000 0.371 0.000
10110 3 7 109.270 1.30107e-20 0.000 0.773 0.000 0.000 0.227
11001 3 7 241.458 0 0.000 0.000 0.729 0.271 -0.000
11010 3 7 236.601 0 0.000 -0.000 1.258 0.000 -0.258 infeasible
11100 3 7 376.541 0 0.000 -0.000 0.000 1.574 -0.574 infeasible
01111 4 8 95.009 4.45451e-17 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 221.266 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 268.973 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 490.465 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1357.083 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.245824 - -
best pat: 00100 0.263635 chi(nested): 1.033 p-value for nested model: 0.309513
best pat: 00101 0.147069 chi(nested): 3.042 p-value for nested model: 0.081157
best pat: 10101 0.000756796 chi(nested): 15.501 p-value for nested model: 8.24733e-05
best pat: 01111 4.45451e-17 chi(nested): 70.003 p-value for nested model: 5.92268e-17



Sintashta (prob: 8.59%; chisq: 8.16):



left pops:
khanabadoshi
Iran_Neolithic
Sintashta
AG3-MA1
Andamanese_Onge
Han

right pops:
Bichon
Chukchi
Karitiana
Kostenki14
Levant_Neolithic-Epipaleolithic
Mbuti
Mota
Papuan
Ust_Ishim


fixed pat wt dof chisq tail prob
00000 0 4 8.161 0.0858584 0.353 0.306 0.070 0.191 0.080
00001 1 5 11.871 0.036601 0.320 0.292 0.130 0.258 -0.000
00010 1 5 17.499 0.00364405 0.320 0.292 0.130 0.258 -0.000
00100 1 5 9.349 0.0959299 0.320 0.292 0.130 0.258 -0.000
01000 1 5 18.201 0.00270456 0.642 -0.000 0.213 0.074 0.070
10000 1 5 21.315 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00011 2 6 31.941 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00101 2 6 16.784 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
00110 2 6 20.811 0 -0.000 0.616 -0.039 0.371 0.052 infeasible
01001 2 6 20.468 0.00228486 0.600 -0.000 0.262 0.138 0.000
01010 2 6 19.982 0.00279037 0.686 -0.000 0.195 -0.000 0.119
01100 2 6 32.349 1.39875e-05 0.804 0.000 -0.000 0.005 0.191
10001 2 6 22.700 0.000903381 0.000 0.587 0.010 0.404 0.000
10010 2 6 93.274 0 0.000 0.824 -0.181 0.000 0.357 infeasible
10100 2 6 21.650 0.00140069 0.000 0.594 0.000 0.370 0.036
11000 2 6 132.804 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
00111 3 7 90.016 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
01011 3 7 34.974 0 -0.000 -0.000 0.819 0.623 -0.441 infeasible
01101 3 7 55.762 1.05271e-09 0.777 -0.000 -0.000 0.223 -0.000
01110 3 7 32.356 3.48911e-05 0.806 -0.000 0.000 0.000 0.194
10011 3 7 160.149 0 0.000 0.519 0.481 0.000 -0.000
10101 3 7 22.733 0.00189669 0.000 0.592 0.000 0.408 0.000
10110 3 7 96.504 5.67869e-18 0.000 0.720 0.000 0.000 0.280
11001 3 7 230.384 0 0.000 0.000 0.741 0.259 -0.000
11010 3 7 226.485 0 0.000 -0.000 1.245 0.000 -0.245 infeasible
11100 3 7 382.347 0 -0.000 -0.000 0.000 1.552 -0.552 infeasible
01111 4 8 91.905 1.908e-16 1.000 -0.000 -0.000 0.000 0.000
10111 4 8 257.944 0 0.000 1.000 0.000 0.000 0.000
11011 4 8 255.435 0 0.000 -0.000 1.000 0.000 0.000
11101 4 8 486.811 0 0.000 -0.000 -0.000 1.000 0.000
11110 4 8 1312.513 0 0.000 -0.000 -0.000 0.000 1.000
best pat: 00000 0.0858584 - -
best pat: 00100 0.0959299 chi(nested): 1.188 p-value for nested model: 0.275729
best pat: 01010 0.00279037 chi(nested): 10.633 p-value for nested model: 0.00111108
best pat: 10101 0.00189669 chi(nested): 2.752 p-value for nested model: 0.0971461
best pat: 01111 1.908e-16 chi(nested): 69.171 p-value for nested model: 9.02729e-17




khana Z282 :: Afanasievo / Poltavka > Samara > Kalmykia > Srubnaya > Corded Ware > Andronovo > Sintashta


This may help in inferring when/where Z283 and Z93 split.

Hey bro, David did a similar test for me. Here are my results.

Iran Neolithic: 45.5
Yamnaya_Kalmykia: 36.2
Dai: 18.2

Has he done this one for you?

CatsRule
09-06-2018, 11:56 PM
I think modern Western Iranians have ~90% genetic continuity to Sassanian era, I feel. We cannot conclusively establish this without actual Sassanian samples, but there does not seem to be as admixture with others as is frequently claimed. Modern Eastern Iranians like Tajiks have about 90% genetic continuity with Bactrians or Sogdians, and we have actual samples that show this.

A lot of confusion arises because many people do not take time to distinguish Western and Eastern Iranian ancestries. They were racially different but on an ethnocultural continuum.

Moe12
09-08-2018, 08:24 PM
Well, foreign blood is certainly there, but I'd say Iranian Persians are definitely descendants of the ancient Persians.

CatsRule
09-10-2018, 12:54 AM
Well, foreign blood is certainly there, but I'd say Iranian Persians are definitely descendants of the ancient Persians.

Depending on region, it can range from 5 to 15% foreign admixture, but typically, it is not more than 10%.

Moe12
09-10-2018, 11:56 AM
Depending on region, it can range from 5 to 15% foreign admixture, but typically, it is not more than 10%.

Agreed! And I think this also can apply to Iranian farmers and Aryan invaders?

CatsRule
09-11-2018, 03:32 AM
Agreed! And I think this also can apply to Iranian farmers and Aryan invaders?

Iranians can largely be modeled as a mixture between Chalcolithic Iranian farmers and the Sintashta Aryan invaders. Most Iranians have like 20-25% steppe admixture.

yelmex
09-11-2018, 09:21 PM
Most "foreign" admixture can be traced back to migrations from the Caucasus some time during Iran's aged history if I am not mistaken.

Dorkymon
09-11-2018, 09:26 PM
There is significant evidence that suggests that modern Iranians have elevated Middle Eastern and South Asian ancestry, and in the case of the Bandaris, African ancestry.

Surely, it's the other way around. The ancient inhabitants of the Iranian plateau had way more Caucasus and South Asian-related ancestry and the modern pull to the North could be attributed to the Indo-Europeans who also brought the language.

Just look at the Elamites.

Kurd
09-12-2018, 01:51 AM
Iranians can largely be modeled as a mixture between Chalcolithic Iranian farmers and the Sintashta Aryan invaders. Most Iranians have like 20-25% steppe admixture.

I would presume they would genetically be similar to the Kurds (Feyli & Kurmanji), If that is the case, then they will also need Turkic in addition to Iran-Chl and Sintashta, because neither Iran-Chl nor Sintashta had the levels of E Asian modern Iranians and Kurds have. This increase in E Asian admixture in present day Kurds and Iranian happened after the Bronze Age, and is courtesy of the numerous admixture pulses into the Iranian plateau from Central Asia and the Caucasus.

Table 5 at http://www.eurasiandna.com/2018/07/01/impact-of-the-iron-age-saka-and-scythians-on-south-west-asian-demography/ gives you an idea of the amount of Iran-Chl, Sintashta, and Turkic in present day Kurds which I don't expect to be much different from present day Iranians.

Edit: Generally speaking there has been a steady rise of E Asian admixture into W Asia over the past 2000 years. This has been facilitated by population growth, increased mobility between E and C Asia and W Asia, and increased trade.

Unfortunately population growth and encroachment on wildlife areas has had a very devastating effect on the wildlife. What a beautiful world it must have been at least from a wildlife perspective with Tigers roaming the Caspian forests, and Asiatic Lions roaming the lowlands and marshes, and Asiatic Cheetahs in the 1000s roaming the plains, along with numerous other wildlife now extinct on the verge of extinction thanks to human population explosion and hunting.

It is inevitable that ethnic lines will become very blurred in the future with urbanization, technology facilitating travel across large distances, and population explosion.

Helves
09-13-2018, 09:48 PM
Has anyone adressed the Levantine input in modern Iranians(and Kurds I presume) in comparison with the chalcolithic samples we have so far from Iran?

"distance%=0.8903"

Iranian_Zoroastrian

Gonur1_BA,42.6
Levant_BA_North,32
Sintashta_MLBA,16.2
Hajji_Firuz_ChL,7.6
Turk_Medieval,1.6

"distance%=0.8766"

Iranian_Lor

Gonur1_BA,33
Levant_BA_North,27.6
Hajji_Firuz_ChL,26.4
Sintashta_MLBA,8
Turk_Medieval,5

Without Levant_BA_North. Still good fits, but much worse than the previous ones.

"distance%=1.844"

Iranian_Zoroastrian

Hajji_Firuz_ChL,54.6
Gonur1_BA,25
Sintashta_MLBA,16.2
Turk_Medieval,4.2

"distance%=1.645"

Iranian_Lor

Hajji_Firuz_ChL,67
Gonur1_BA,17.8
Sintashta_MLBA,8
Turk_Medieval,7.2

I suspect that Late Bronze Age/Early Iron Age Western Iran was more Levantine/SW Asian shifted than the Seh Gabi samples we have so far. The Iron Age NW Iranian also has a good chunk of it.

"distance%=2.6403"

Hasanlu_IA

Hajji_Firuz_ChL,37.2
Gonur1_BA,27.6
Levant_BA_North,24.2
Sintashta_MLBA,11

Kurd
09-14-2018, 02:44 AM
Has anyone adressed the Levantine input in modern Iranians(and Kurds I presume) in comparison with the chalcolithic samples we have so far from Iran?

"distance%=0.8903"

Iranian_Zoroastrian

Gonur1_BA,42.6
Levant_BA_North,32
Sintashta_MLBA,16.2
Hajji_Firuz_ChL,7.6
Turk_Medieval,1.6

"distance%=0.8766"

Iranian_Lor

Gonur1_BA,33
Levant_BA_North,27.6
Hajji_Firuz_ChL,26.4
Sintashta_MLBA,8
Turk_Medieval,5

Without Levant_BA_North. Still good fits, but much worse than the previous ones.

"distance%=1.844"

Iranian_Zoroastrian

Hajji_Firuz_ChL,54.6
Gonur1_BA,25
Sintashta_MLBA,16.2
Turk_Medieval,4.2

"distance%=1.645"

Iranian_Lor

Hajji_Firuz_ChL,67
Gonur1_BA,17.8
Sintashta_MLBA,8
Turk_Medieval,7.2

I suspect that Late Bronze Age/Early Iron Age Western Iran was more Levantine/SW Asian shifted than the Seh Gabi samples we have so far. The Iron Age NW Iranian also has a good chunk of it.

"distance%=2.6403"

Hasanlu_IA

Hajji_Firuz_ChL,37.2
Gonur1_BA,27.6
Levant_BA_North,24.2
Sintashta_MLBA,11


These results are not consistent with formal stats.

1- You should go with the results that make sense, and not with lowest fit. In this case, for Indo-Iranians such as Kurds and Persians it doesn't make sense that Levant-BA admixture is equal to or greater than Iran-Chl

2- I realize you use nMonte because its easy and you feel comfortable using it, but you really should learn how to use formal stats,so that if something doesn't make sense, you can go and check it with formal stats. Research papers rely on formal stats and not nMonte. qpAdm for example is informative to introgression and not simply common ancestry such as likely the case with nMonte.

Anyways, I checked this for Kurds using qpAdm. I can't imagine other Iranians being much different. Kurds C1-C3 are Kurmanjis from N Iraq. and Kurds-F are Feyli.

Here is a summary of the results. If someone is familiar with qpAdm and would like to look at the whole run, let me know and I'll be glad to post it.

Outgroups used:

Mbuti
ShamankaEN
Karitiana
Ust_Ishim
WHG
West_Siberia_N
Anatolia_N
Ganj_Dareh_N
Levant_N
Onge
EHG

1- You will note that all Kurds have reject Levant-BA and have infeasible results with it except for Kurd-C1 which takes a small amount of 5%.

2- You will also note that for about 1/2 the Kurd samples the Medieval Turkic Kipchak amount exceeds the Sintashta admixture amount.

Red rows are infeasible. Green rows are feasible and can't be rejected based on their p-values.



SAMPLE
Haji-Firuz-Chl
Levant-BA
Sintashta-MLBA
Kipchaks
p-value
OUTCOME


Kurd-C1
70.00%
5.10%
16.00%
8.80%
0.96
FEASIBLE


Kurd-C2
74.50%
0.00%
8.70%
16.80%
0.27
FEASIBLE


Kurd-C2
91.70%
-15.50%
8.50%
15.30%

INFEASIBLE


Kurd-C3
71.60%
0.00%
12.50%
15.90%
0.24
FEASIBLE


Kurd-C3
95.00%
-16.30%
12.50%
14.30%

INFEASIBLE


Kurd-F1
72.20%
0.00%
16.10%
11.60%
0.53
FEASIBLE


Kurd-F1
80.50%
-7.20%
15.90%
10.80%

INFEASIBLE


Kurd-F2
62.70%
0.00%
20.60%
16.60%
0.23
FEASIBLE


Kurd-F2
81.30%
-16.40%
19.90%
15.20%

INFEASIBLE


Kurd-F4
76.60%
0.00%
10.10%
13.40%
0.53
FEASIBLE


Kurd-F4
85.20%
-7.40%
9.60%
12.60%

INFEASIBLE


Kurd-F5
70.00%
0.00%
16.70%
13.30%
0.33
FEASIBLE


Kurd-F5
84.90%
-13.50%
16.90%
11.80%

INFEASIBLE


Kurd-F6
68.00%
0.00%
18.10%
13.90%
0.08
FEASIBLE


Kurd-F6
94.80%
-24.40%
18.20%
11.40%

INFEASIBLE


Kurd-F8
71.00%
0.00%
8.40%
20.60%
0.53
FEASIBLE


Kurd-F8
79.40%
-7.20%
7.90%
19.90%

INFEASIBLE

Helves
09-14-2018, 02:54 AM
These results are not consistent with formal stats.

1- You should go with the results that make sense, and not with lowest fit. In this case, for Indo-Iranians such as Kurds and Persians it doesn't make sense that Levant-BA admixture is equal to or greater than Iran-Chl

2- I realize you use nMonte because its easy and you feel comfortable using it, but you really should learn how to use formal stats,so that if something doesn't make sense, you can go and check it with formal stats. Research papers rely on formal stats and not nMonte. qpAdm for example is informative to introgression and not simply common ancestry such as likely the case with nMonte.

Anyways, I checked this for Kurds using qpAdm. I can't imagine other Iranians being much different. Kurds C1-C3 are Kurmanjis from N Iraq. and Kurds-F are Feyli.

Here is a summary of the results. If someone is familiar with qpAdm and would like to look at the whole run, let me know and I'll be glad to post it.

Outgroups used:

Mbuti
ShamankaEN
Karitiana
Ust_Ishim
WHG
West_Siberia_N
Anatolia_N
Ganj_Dareh_N
Levant_N
Onge
EHG

1- You will note that all Kurds have reject Levant-BA and have infeasible results with it except for Kurd-C1 which takes a small amount of 5%.

2- You will also note that for about 1/2 the Kurd samples the Medieval Turkic Kipchak amount exceeds the Sintashta admixture amount.

Red rows are infeasible. Green rows are feasible and can't be rejected based on their p-values.



SAMPLE
Haji-Firuz-Chl
Levant-BA
Sintashta-MLBA
Kipchaks
p-value
OUTCOME


Kurd-C1
70.00%
5.10%
16.00%
8.80%
0.96
FEASIBLE


Kurd-C2
74.50%
0.00%
8.70%
16.80%
0.27
FEASIBLE


Kurd-C2
91.70%
-15.50%
8.50%
15.30%

INFEASIBLE


Kurd-C3
71.60%
0.00%
12.50%
15.90%
0.24
FEASIBLE


Kurd-C3
95.00%
-16.30%
12.50%
14.30%

INFEASIBLE


Kurd-F1
72.20%
0.00%
16.10%
11.60%
0.53
FEASIBLE


Kurd-F1
80.50%
-7.20%
15.90%
10.80%

INFEASIBLE


Kurd-F2
62.70%
0.00%
20.60%
16.60%
0.23
FEASIBLE


Kurd-F2
81.30%
-16.40%
19.90%
15.20%

INFEASIBLE


Kurd-F4
76.60%
0.00%
10.10%
13.40%
0.53
FEASIBLE


Kurd-F4
85.20%
-7.40%
9.60%
12.60%

INFEASIBLE


Kurd-F5
70.00%
0.00%
16.70%
13.30%
0.33
FEASIBLE


Kurd-F5
84.90%
-13.50%
16.90%
11.80%

INFEASIBLE


Kurd-F6
68.00%
0.00%
18.10%
13.90%
0.08
FEASIBLE


Kurd-F6
94.80%
-24.40%
18.20%
11.40%

INFEASIBLE


Kurd-F8
71.00%
0.00%
8.40%
20.60%
0.53
FEASIBLE


Kurd-F8
79.40%
-7.20%
7.90%
19.90%

INFEASIBLE


I trust you, but that's awfully a lot of medieval Turkish for Kurds isn't it? I don't think I've seen Kurds scoring more than 1-2% Siberian on most ADMIXTURE runs.
Might be different samples aswell , I think Levant_BA in your run is the older one from Jordan, whilst I'm using the ones from Sidon. They were quite different.

Kurd
09-14-2018, 03:02 AM
I trust you, but that's awfully a lot of medieval Turkish for Kurds isn't it? I don't think I've seen Kurds scoring more than 1-2% Siberian on most ADMIXTURE runs.
Might be different samples aswell , I think Levant_BA in your run is the older one from Jordan, whilst I'm using the ones from Sidon. They were quite different.

You are welcome to see the full output. Just let me know which samples, and I can post them.

Yes, 1-2% is what gedmatch calculators show, but the problem is that their W Eurasian references such as Caucasians Iranians and some of their E European references are themselves E Asian admixed. So basically anything above 1-2% E Asian is hidden in those W Eurasian references which themselves received E Asian geneflow mostly post the Bronze-Age.

That is the reason I wrote this article to show the hidden E Asian admixture:

http://www.eurasiandna.com/2018/08/18/how-to-interpret-your-ancestry-admixture-results/

(http://www.eurasiandna.com/2018/08/18/how-to-interpret-your-ancestry-admixture-results/)

So the Kipchak amount accounts for the accumulated E Admixture absorbed by Iranics such as Kurds from all the admixture pulses originating in Central Asia over the past 4000 years.

kyp.durrron
09-25-2018, 07:12 AM
I saw a figure placing modern Iranians between neolithic Iranians and neolithic Anatolian farmers. They also showed a slight shift to Eurasian HG. Pakistanis and Afghans were actually closer to Neolithic Iranians than modern iranians (except Zoroastrians).
Keep in mind that neolithic NW-Iranians (Hasanlu) did not fall into a cluster with the other Neolitic Iranians. Instead they were pretty close to modern Iranians.

Ebizur
10-12-2019, 02:46 AM
Supplementary Table 3 and Supplementary Table 4 of Karafet et al. 2018 ("Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations") contain information regarding the Y-DNA of a substantial sample (n=136) of Iranians (Composite samples, Iran; "Language Family"=Indo-European/Indo-Iranian/Persian). I do not recall having seen data regarding this sample of Iranian Y-DNA in any previous publication. Does anyone recognize this sample?

18 Iranian/Composite samples, Iran
8/136 = 5.9% E-M123
1/136 = 0.7% E-V12
2/136 = 1.5% E-V13
5/136 = 3.7% E-V22
1/136 = 0.7% E-P1
17/136 = 12.5% E total

5/136 = 3.7% G-M285
2/136 = 1.5% G-P15(xL30,L91)
1/136 = 0.7% G-L30(xP303,L90)
1/136 = 0.7% G-L90
2/136 = 1.5% G-P303*
11/136 = 8.1% G-M201 total

1/136 = 0.7% F-M578(xK-M9, G-M201, J-M304)
2/136 = 1.5% H1a1-M52
1/136 = 0.7% I2a2a-M223/P222

6/136 = 4.4% J1-M267(xJ1a2a1a-L136)
3/136 = 2.2% J1a2a1a-L136(xJ1a2a1a2-P58)
11/136 = 8.1% J1a2a1a2b-L147
20/136 = 14.7% J1-M267 total

3/136 = 2.2% J2a-M410(xP354)
9/136 = 6.6% J2a1-L27(xJ2a1h-L24, J2a1b-M67, J2a1a-M322)
5/136 = 3.7% J2a1h2-L25(xJ2a1h2a1-L70)
1/136 = 0.7% J2a1h2a1-L70(xJ2a1h2a1b-M318)
5/136 = 3.7% J2a1a-M47
2/136 = 1.5% J2a1b-M67(xJ2a1b1-M92)
4/136 = 2.9% J2a1b1-M92
29/136 = 21.3% J2a-M410 total

2/136 = 1.5% J2b-M12
31/136 = 22.8% J2-M172 total

1/136 = 0.7% L-M20(?xM76, M317, M357)
2/136 = 1.5% L1a1-M76
3/136 = 2.2% L1b-M317
6/136 = 4.4% L-M20 total

1/136 = 0.7% N1a2b-P43*
1/136 = 0.7% O1a1a-P203(xM101)

1/136 = 0.7% Q-P36(xQ1b-L474, Q1a2-M25, Q2a1-M378, Q1a1-NWT1)
3/136 = 2.2% Q2a1-M378
1/136 = 0.7% Q1b-M346*
5/136 = 3.7% Q-P36 total

3/136 = 2.2% R2a-M124

2/136 = 1.5% R1-M173(xR1b1-L278, R1a1a-M515)
4/136 = 2.9% R1a1a1b1a-Z282
16/136 = 11.8% R1a1a1b2-Z93
22/136 = 16.2% R1-M173(xR1b1-L278) total

6/136 = 4.4% R1b1-L278(xR1b1a1a-P297)
1/136 = 0.7% R1b1a1a1-M73
2/136 = 1.5% R1b1a1a2-M269(xR1b1a1a2a-L23)
5/136 = 3.7% R1b1a1a2a-L23(xR1b1a1a2a1a-P311)
14/136 = 10.3% R1b1-L278 total

1/136 = 0.7% T1a1-S21(Page21)*(?xT1a1a-S2(Page2))

Iranian members of Y-DNA haplogroup R1b seem to be only distantly related to most Western European members of this haplogroup. The six Iranian R1b1-L278(xR1b1a1a-P297) individuals all carry identical or very similar Y-STR haplotypes, so they probably all belong to only one of the following subclades: R1b1b-PH155, R1b1a2-V88, or R1b1a1b-V1636.

This study's sample of Uyghurs from Xinjiang (n=66) includes seven members of R1b1-L278(xR1b1a1a-P297). The Y-STR haplotypes of these Uyghur individuals are more diverse among themselves compared to the Y-STR haplotypes of the Iranian individuals, and none of them appears to be particularly closely related to the Iranians. There is also one R1b1-L278(xR1b1a1a-P297) individual in this study's sample of Manchus (n=50); this Manchu individual's haplotype does not seem particularly similar to that of any of the Iranians or Uyghurs.

This study's two R1-M173(xR1b1-L278, R1a1a-M515) Iranian individuals carry similar Y-STR haplotypes, so they probably both belong to the same subclade of R1a(xR1a1a-M515/M17), such as R1a2-YP4141 or R1a1b-YP1272.

Ebizur
10-12-2019, 05:30 AM
Also from Tatiana M. Karafet, Ludmila P. Osipova, Olga V. Savina et al. (2018), "Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations": a possible instance of Y-DNA haplogroup I1 in a Tajik from Tajikistan.

20 Tajik/Tajikistan
1/15 C2c1-P323(xC2c1a1a1-M407) (NEVGEN prediction based on 12-loci Y-STR haplotype: C2 M217> F1067, Probability 57.09, Fitness 41.09, Fitness 2 0.86) "Warning: Values of fitness (or relative fitness) are rather small, so results are not too confident. It is possible that its haplogroup is not supported by current version of predictor, or haplotype really belong to some supported haplogroup, but it is rare or too distant branch, which is not sufficiently represented in samples used by predictor."
1/15 E1b1b1a1-M78(xE1b1b1a1a1-V12, E1b1b1a1b1a-V13, E1b1b1a1b2-V22) (NEVGEN prediction based on 12-loci Y-STR haplotype: E1b1b (for 67+ markers, try level for E-s, 60+ subclades), Probability 79.48, Fitness 28.23, Fitness 2 0.63) "Warning: Values of fitness (or relative fitness) are rather small, so results are not too confident. It is possible that its haplogroup is not supported by current version of predictor, or haplotype really belong to some supported haplogroup, but it is rare or too distant branch, which is not sufficiently represented in samples used by predictor."
1/15 I1-P30 (NEVGEN prediction based on 12-loci Y-STR haplotype: I1, Probability 99.89, Fitness 46.45, Fitness 2 0.82) "Warning: Values of fitness (or relative fitness) are rather small, so results are not too confident. It is possible that its haplogroup is not supported by current version of predictor, or haplotype really belong to some supported haplogroup, but it is rare or too distant branch, which is not sufficiently represented in samples used by predictor."
2/15 J2a1-L27(xJ2a1h-L24, J2a1b-M67, J2a1a-M322)
1/15 J2a1h-L24(xJ2a1h2-L25)
1/15 J2a1a-M47/M322
1/15 J2a1b-M67(xJ2a1b1-M92)
1/15 O-P196(xO1a-M119, O1b-P31, O2-M122, O2-P198) (NEVGEN prediction based on 12-loci Y-STR haplotype: O1b1 F2320, Probability 48.82, Fitness 43.5, Fitness 2 0.88) "Warning: Values of fitness (or relative fitness) are rather small, so results are not too confident. It is possible that its haplogroup is not supported by current version of predictor, or haplotype really belong to some supported haplogroup, but it is rare or too distant branch, which is not sufficiently represented in samples used by predictor."
1/15 O2a2b1-M134 (NEVGEN prediction based on 12-loci Y-STR haplotype: O2a2 F525, Probability 98.53, Fitness 56.09, Fitness 2 1.4) "Warning: Values of fitness (or relative fitness) are rather small, so results are not too confident. It is possible that its haplogroup is not supported by current version of predictor, or haplotype really belong to some supported haplogroup, but it is rare or too distant branch, which is not sufficiently represented in samples used by predictor."
1/15 Q-P36(xQ1b-L474, Q1a2-M25, Q2a1-M378, Q1a1-NWT1) (NEVGEN prediction based on 12-loci Y-STR haplotype: Q L275>> L245, Probability 99.51, Fitness 63.83, Fitness 2 1.01) "Warning: Values of fitness (or relative fitness) are rather small, so results are not too confident. It is possible that its haplogroup is not supported by current version of predictor, or haplotype really belong to some supported haplogroup, but it is rare or too distant branch, which is not sufficiently represented in samples used by predictor."
2/15 Q1a2-M25
2/15 R1a1a1b2-Z93

Other curious results from this small sample of Tajiks include the E1b1b1a1-M78(xE1b1b1a1a1-V12, E1b1b1a1b1a-V13, E1b1b1a1b2-V22) and the O-P196(xO1a-M119, O1b-P31, O2-M122, O2-P198).

C2c1-P323(xC2c1a1a1-M407) belongs to the typically East/Southeast Asian (Manchu, Chinese, Tibetan, Korean, Japanese, Vietnamese, Tai, etc.) C2c1-P323 branch of C2-M217, but not to its typically Central Eurasian (northern/western Mongolic in particular) C2c1a1a1-M407 subclade.