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Krefter
08-22-2015, 04:53 PM
Part 1: Looking For mtDNA Diversity in West Eurasia (http://mtdnaatlas.blogspot.com/2015/08/looking-for-mtdna-diversity-in-west.html): My post is at my new Blog: mtDNA Atlas (http://mtdnaatlas.blogspot.com/).

The purpose of my Blog is to "Providing a database of Human mtDNA from around the World". This is just the start. I'll eventually get data from every part of the globe.

As it says in the Title this is only Part 1. My first post is just for showing the diversity of mtDNA that exists in West Eurasia. In my next posts about West Eurasian mtDNA I'll look for founder effects, shared unique mutations between differnt populations, theoretical origins of certain mtDNA, and more.

J Man
08-23-2015, 12:10 PM
Sounds good! I am looking forward to following this thread and your findings.

evon
08-23-2015, 12:51 PM
If you need any help with regards to mtDNA G2a and U5b1b1 in Europe let me know, as I have done a fair amount of research on these mtDNA lines..

I have also started to look into Romani mtDNA T1a and M5's etc...

J Man
08-23-2015, 03:14 PM
Part 1: Looking For mtDNA Diversity in West Eurasia (http://mtdnaatlas.blogspot.com/2015/08/looking-for-mtdna-diversity-in-west.html): My post is at my new Blog: mtDNA Atlas (http://mtdnaatlas.blogspot.com/).

The purpose of my Blog is to "Providing a database of Human mtDNA from around the World". This is just the start. I'll eventually get data from every part of the globe.

As it says in the Title this is only Part 1. My first post is just for showing the diversity of mtDNA that exists in West Eurasia. In my next posts about West Eurasian mtDNA I'll look for founder effects, shared unique mutations between differnt populations, theoretical origins of certain mtDNA, and more.

Do you think that it would be possible to sort West Eurasian mtDNA haplogroups into WHG, EHG, EEF and Near Eastern Neolithic categories?

Krefter
08-23-2015, 11:21 PM
Do you think that it would be possible to sort West Eurasian mtDNA haplogroups into WHG, EHG, EEF and Near Eastern Neolithic categories?

No, but there are trends. Obviously U5, U4, and U2e are mostly WHG/EHG markers. And most U5b is probably WHG and most U5a/U4/U2e is probably EHG. But U5b existed in Yamnaya and U5a/U4 existed in Neolithic farmers. There's Near Eastern package of haplogroups(R0, UK, JT, N1, N2, X). All Western lineages except a handful for U lineages and maybe others are probably of Near Eastern origin. I think T2b, J1c, H1, H3, and HV0 might specifically be Neolithic Anatolian/East Mediterranean lineages.

Also I just want to say too much emphasis is put on haplogroup H. There's no basis in treating H in Europe as more special than JT for example. Not much is known about the geographic/diversity of H. We need 1,000s of fully-sequenced Hs from West Eurasia to understand its history. If H shows a great amount of diversity and age in Europe, then yes it is special, but people have been calling it special for over 10 years just because it has frequency of 40%. Early Neolithic farmers had a high frequency of H1/H3 like modern Europeans. There's no way their H1/H3 came from hunter gatherers. They brought it from the Near East. H should be included with JT, N1, N2, X as a Near Eastern lineage.

And I'm tired of people believing in a myth of some type of "H people"(eg, Bell beaker) who traveled across Europe and made sure everyone had 40% H. That never happened. It's completely random everyone has 40% H.

J Man
08-23-2015, 11:35 PM
No, but there are trends. Obviously U5, U4, and U2e are mostly WHG/EHG markers. And most U5b is probably WHG and most U5a/U4/U2e is probably EHG. But U5b existed in Yamnaya and U5a/U4 existed in Neolithic farmers. There's Near Eastern package of haplogroups(R0, UK, JT, N1, N2, X). All Western lineages except a handful for U lineages and maybe others are probably of Near Eastern origin. I think T2b, J1c, H1, H3, and HV0 might specifically be Neolithic Anatolian/East Mediterranean lineages.

Also I just want to say too much emphasis is put on haplogroup H. There's no basis in treating H in Europe as more special than JT for example. Not much is known about the geographic/diversity of H. We need 1,000s of fully-sequenced Hs from West Eurasia to understand its history. If H shows a great amount of diversity and age in Europe, then yes it is special, but people have been calling it special for over 10 years just because it has frequency of 40%. Early Neolithic farmers had a high frequency of H1/H3 like modern Europeans. There's no way their H1/H3 came from hunter gatherers. They brought it from the Near East. H should be included with JT, N1, N2, X as a Near Eastern lineage.

And I'm tired of people believing in a myth of some type of "H people"(eg, Bell beaker) who traveled across Europe and made sure everyone had 40% H. That never happened. It's completely random everyone has 40% H.

I agree with you completely in pretty much everything you say here. Definitely for years now to much emphasis has been put on haplogroup H. H is such a large super-haplogroup that really it is the subclades such as H1, H2, H3 etc. that need to be looked at. Saying just ''H'' this and ''H'' that (Maju comes to mind) is pretty much useless. So you think for sure then that the mtDNA haplogroup H subclades H1 and H3 came to Europe with Anatolian or East Mediterranean Neolithic farmers?

paulgill
08-23-2015, 11:44 PM
.......................

jeanL
08-24-2015, 01:21 AM
Early Neolithic farmers had a high frequency of H1/H3 like modern Europeans. There's no way their H1/H3 came from hunter gatherers. They brought it from the Near East. H should be included with JT, N1, N2, X as a Near Eastern lineage.

And I'm tired of people believing in a myth of some type of "H people"(eg, Bell beaker) who traveled across Europe and made sure everyone had 40% H. That never happened. It's completely random everyone has 40% H.

Where is the data to back that claim?

Krefter
08-24-2015, 07:01 AM
Where is the data to back that claim?

Here. Sorry it is messy, I was editing it today and did not finish.

https://docs.google.com/spreadsheets/d/1HcAhe7QvggT792VruuoZX6IsTg4LhWXV-Z_ZfTk2KGA/edit#gid=1405879894

Of Neolithic H samples tested for an H1 and H3 SNP.

3/10 H1 from LBK
10/20 have H1 and 4/20 have H3 from Early Neolithic France
3/6 have H1 and 3/6 have H3 from Middle Neolithic France.
2/4 have H3 and 1/4 have H1 from Middle Neolithic Central Europe.
1/1 have H1 from Megalithic Spain.

But from Yamnaya/Catacomb.
2/19 are H1 and 0/19 are H3.

J Man
08-24-2015, 10:19 AM
Krefter...Where and when do you think the U5 subclade U5b2c originated? With which cultural group(s)?

Krefter
08-24-2015, 11:26 PM
Krefter...Where and when do you think the U5 subclade U5b2c originated? With which cultural group(s)?

Besides it being a WHG lineage I know nothing. With fully-sequenced U5b2cs things about its history can be learned, but we don't have that yet. U5b2c can't be defined with just HV1+2 coverage, so I don't know if my U5b samples are U5b2c or not. U5b2c2b though is defined by HV1, and my only sample that is U5b2c2b is from Ireland like your U5b2c2 is.

I2a1-P37(xM26) as far as I know is most popular in the British Isles. So, maybe their I2-P37, U5b2c, and other lineages are from Mesolithic Brits and Irish who were assimilated into Neolithic farmer communities, and later IE R1b-L21 Bronze age groups immigrating from continental Europe. It would totally make sense that your U5b2c2 is from Irish versions of La Brana-1.

khanabadoshi
08-25-2015, 12:49 AM
Besides it being a WHG lineage I know nothing. With fully-sequenced U5b2cs things about its history can be learned, but we don't have that yet. U5b2c can't be defined with just HV1+2 coverage, so I don't know if my U5b samples are U5b2c or not. U5b2c2b though is defined by HV1, and my only sample that is U5b2c2b is from Ireland like your U5b2c2 is.

I2a1-P37(xM26) as far as I know is most popular in the British Isles. So, maybe their I2-P37, U5b2c, and other lineages are from Mesolithic Brits and Irish who were assimilated into Neolithic farmer communities, and later IE R1b-L21 Bronze age groups immigrating from continental Europe. It would totally make sense that your U5b2c2 is from Irish versions of La Brana-1.

I believe the Jammuite-Kashmiri user, Bored, has a mtDNA U lineage that peaks in the Kalash. You most definitely should get in touch with him.

And as a side note, mtDNA is rarely looked at in depth. I don't have enough knowledge to know why this is so, perhaps there is a reason? All I know is, I can find much more on my rare y-DNA than my rare mtDNA. Truthfully, this is very annoying...as both have equal relevance. Tbh... I joined such sites to find out more about my mtDNA not so much my y-DNA.

paulgill
08-25-2015, 02:08 AM
I believe the Jammuite-Kashmiri user, Bored, has a mtDNA U lineage that peaks in the Kalash. You most definitely should get in touch with him.

And as a side note, mtDNA is rarely looked at in depth. I don't have enough knowledge to know why this is so, perhaps there is a reason? All I know is, I can find much more on my rare y-DNA than my rare mtDNA. Truthfully, this is very annoying...as both have equal relevance. Tbh... I joined such sites to find out more about my mtDNA not so much my y-DNA.

Though I am not sure if Kalash and Bored lineage is Eurasian, but lot many Indians have the U maternal lineage, generally, it is not the same as the European one, only very distantly related to it. I had also posted mine here earlier but then realized that he was not interested in the West Asian but West Eurasian, I had misread the title, so I deleted it.

Also mtDNA mutates much slower than the yDNA, thus is not of great importance in genealogy, again most cultures are patrilineage thus are interested in the yDNA more than the mtDNA.

parasar
08-25-2015, 03:35 PM
No, but there are trends. Obviously U5, U4, and U2e are mostly WHG/EHG markers. And most U5b is probably WHG and most U5a/U4/U2e is probably EHG. But U5b existed in Yamnaya and U5a/U4 existed in Neolithic farmers. There's Near Eastern package of haplogroups(R0, UK, JT, N1, N2, X). All Western lineages except a handful for U lineages and maybe others are probably of Near Eastern origin. I think T2b, J1c, H1, H3, and HV0 might specifically be Neolithic Anatolian/East Mediterranean lineages.

Also I just want to say too much emphasis is put on haplogroup H. There's no basis in treating H in Europe as more special than JT for example. Not much is known about the geographic/diversity of H. We need 1,000s of fully-sequenced Hs from West Eurasia to understand its history. If H shows a great amount of diversity and age in Europe, then yes it is special, but people have been calling it special for over 10 years just because it has frequency of 40%. Early Neolithic farmers had a high frequency of H1/H3 like modern Europeans. There's no way their H1/H3 came from hunter gatherers. They brought it from the Near East. H should be included with JT, N1, N2, X as a Near Eastern lineage.

And I'm tired of people believing in a myth of some type of "H people"(eg, Bell beaker) who traveled across Europe and made sure everyone had 40% H. That never happened. It's completely random everyone has 40% H.

We have to keep in mind that Karelians had mtDNA H.
I doubt that Karelians had any Early Neolithic Farmer influence - perhaps someone could run D-stats to check.

Ebizur
08-25-2015, 04:39 PM
We have to keep in mind that Karelians had mtDNA H.
I doubt that Karelians had any Early Neolithic Farmer influence - perhaps someone could run D-stats to check.That is another important point to keep in mind, but the fact remains that mtDNA haplogroup H is much less internally diverse than, say, mtDNA haplogroup U. Haplogroup H is rather comparable to one of the many branches of haplogroup U, such as K. Outside of Western Eurasia, H is similar in diversity to e.g. D4g'1 (the haplogroup that includes American D1 and East Asian D4g). I estimate that haplogroup H is probably just slightly older than the split between the ancestors of Americans and the ancestors of East Asians, perhaps 25,000 years old. At about 20,000 YBP, there lived perhaps as few as seven women belonging to haplogroup H who have produced direct matrilineal descendants among extant humans.

Of course, the close relatives of haplogroup H (HV0'V, HV1, HV2, and R0 somewhat further back) are all likewise spread among so-called "Western Eurasians." Therefore, it is probably nothing too exotic, but any archaeological pattern that one might wish to associate with the spread of haplogroup H really must be much more recent (I would say approximately half the age, or even less than that) than whatever event one associates with the initial spread of haplogroup U.

Gravetto-Danubian
08-25-2015, 04:57 PM
The finding of mtDNA H in Karelia might be the correlate of y group R1 expanding in the post-glacial period from somewhere in Asia where there weren't those "basal eurasian" proto-farmers. Ie basically anywhere between the Caspian and the Himalayas.. .

J Man
08-25-2015, 05:10 PM
We have to keep in mind that Karelians had mtDNA H.
I doubt that Karelians had any Early Neolithic Farmer influence - perhaps someone could run D-stats to check.

That is exactly why we should stop saying just "H" and should really look at subclades. The H subclade in Mesolithic Karelia from what I have read is H2 which most likely has a very different history compared to other H subclades such as H1 and H3.

parasar
08-25-2015, 05:53 PM
That is exactly why we should stop saying just "H" and should really look at subclades. The H subclade in Mesolithic Karelia from what I have read is H2 which most likely has a very different history compared to other H subclades such as H1 and H3.

I agree. Different H lines may have different distributions but ultimately H has to originate in one place.
Didn't we have an H1 from mesolithic Portugal?

J Man
08-25-2015, 06:24 PM
I agree. Different H lines may have different distributions but ultimately H has to originate in one place.
Didn't we have an H1 from mesolithic Portugal?

It does not matter so much where H itself originated. What matters more in this case is where certain subclades originated. The so called H1 sample from Mesolithic Portugal is unreliable and probably contaminated. We need a lot more ancient DNA from UP and Mesolithic Iberia.

Ebizur
08-25-2015, 06:37 PM
That is exactly why we should stop saying just "H" and should really look at subclades. The H subclade in Mesolithic Karelia from what I have read is H2 which most likely has a very different history compared to other H subclades such as H1 and H3.H2 represents the descendants of one of those seven ancient H ancestors to whom I have referred in my previous comment. She may have become separated from the other members of haplogroup H as early as 22,000 YBP, and the distribution of her modern descendants does seem to be centered roughly in Russia proper, so it would be rather fitting if that Mesolithic individual from Karelia belonged to H2. Is it known whether the Mesolithic Karelian specimen belongs to the subclade H2a or H2b?

J Man
08-25-2015, 06:47 PM
H2 represents the descendants of one of those seven ancient H ancestors to whom I have referred in my previous comment. She may have become separated from the other members of haplogroup H as early as 22,000 YBP, and the distribution of her modern descendants does seem to be centered roughly in Russia proper, so it would be rather fitting if that Mesolithic individual from Karelia belonged to H2. Is it known whether the Mesolithic Karelian specimen belongs to the subclade H2a or H2b?

H2a I think.

parasar
08-25-2015, 07:39 PM
It does not matter so much where H itself originated. What matters more in this case is where certain subclades originated. The so called H1 sample from Mesolithic Portugal is unreliable and probably contaminated. We need a lot more ancient DNA from UP and Mesolithic Iberia.

How about the other H?
They can't be all contaminated, right?
We have H in Mesolithic Iberia, Greece, and Karelia. If the Red Lady (Paviland, CRS) turns out H, essentially all of Europe would be covered.
If the folk who proposed the Neolithic entry of H theory are no longer sure, it is time to reassess, or at least limit.
Guido Brandt, Anna Szecsenyi-Nagy, Christina Roth, Kurt Werner, Wolfgang Haak
Human paleogenetics of Europe e The known knowns and the known
unknowns

This picture becomes more complex
with the observation of non-U lineages in peripheral regions in
the far West (haplogroup H and N*) and Northern Russia (haplogroup
H and C), while these are absent in Central European foragers.
Haplogroup H has been reported with high frequencies (38%)
from hunter-gatherers in Portugal and the Basque country
(Chandler et al., 2005; Hervella et al., 2012) and one individual from
the Yuzhnyy Oleni Ostrov site in Northern Karelia (Der Sarkissian
et al., 2013), indicating a widespread and possibly clinal distribution
of haplogroup H in Mesolithic Europe. Under this hypothesis it
seems to be a question of time when the first H lineage will be
reported from Central European hunter-gatherers.




The hunter–gatherers from the Northern of the Iberian Peninsula also showed a high frequency value for haplogroup U but they differentiated from the other European groups by a relatively high frequency for haplogroup H.

http://www.anthrogenica.com/showthread.php?4246-19000-year-old-mt-DNA-Haplogroup-H-from-the-Franco-Cantabrian-site-of-el-Miron!!!!
http://i1133.photobucket.com/albums/m582/jeanlohizun/de.la.rua.et.al2015-Table-1_zpsyxcsojlp.jpg

Ebizur
08-25-2015, 07:54 PM
H2a I think.Thank you. The genealogical split between H2a and H2b should have occurred approximately 15,000 years ago, so I figured the specimen should most likely belong to one or the other subclade.

Has there been any attestation of H2b in remains more ancient than those of early medieval Angles and Lombards?

Krefter
08-25-2015, 08:30 PM
How about the other H?
They can't be all contaminated, right?
We have H in Mesolithic Iberia, Greece, and Karelia. If the Red Lady (Paviland, CRS) turns out H, essentially all of Europe would be covered.
If the folk who proposed the Neolithic entry of H theory are no longer sure, it is time to reassess, or at least limit.
Guido Brandt, Anna Szecsenyi-Nagy, Christina Roth, Kurt Werner, Wolfgang Haak


The chances of a big percentage of H in Europe today being of Mesolithic origin is low. The only chance a decent percentage is, is if small pockets or regions of unsampled hunter gatherers were rich in H. Most Mesolithic ancestry for most Europeans is probably from Central and East Europe, not Iberia. Greek hunter gatherers don't count because they may have had Basal Eurasian.

Krefter
08-25-2015, 08:30 PM
Thank you. The genealogical split between H2a and H2b should have occurred approximately 15,000 years ago, so I figured the specimen should most likely belong to one or the other subclade.

Has there been any attestation of H2b in remains more ancient than those of early medieval Angles and Lombards?

He had HVR1 motof 16291. It's found in several H subclades including H2a2b. H2a2b makes the most sense but it hasn't been confirmed.

J Man
08-25-2015, 08:34 PM
How about the other H?
They can't be all contaminated, right?
We have H in Mesolithic Iberia, Greece, and Karelia. If the Red Lady (Paviland, CRS) turns out H, essentially all of Europe would be covered.
If the folk who proposed the Neolithic entry of H theory are no longer sure, it is time to reassess, or at least limit.
Guido Brandt, Anna Szecsenyi-Nagy, Christina Roth, Kurt Werner, Wolfgang Haak
Human paleogenetics of Europe e The known knowns and the known
unknowns




http://www.anthrogenica.com/showthread.php?4246-19000-year-old-mt-DNA-Haplogroup-H-from-the-Franco-Cantabrian-site-of-el-Miron!!!!
http://i1133.photobucket.com/albums/m582/jeanlohizun/de.la.rua.et.al2015-Table-1_zpsyxcsojlp.jpg

I still do not see any pre-Neolithic H1 or H3 among those samples listed above although I must admit that I do not know mtDNA haplogroup mutations very well. I do see a pre-Neolithic H6 and H though. Indeed some H probably was present in Europe before the Neolithic but a lot also came to Europe with Neolithic farmers from Anatolia/Near East I think. Like I said before we need to look at SUBCLADES not just ''H''!...Look at mtDNA haplogroup U. Only certain subclades existed in UP and Mesolithic Europe. Those subclades are U5, U4 and U2. Other U subclades such as U1, U3 and K came later with Neolithic farmers or even later than that in some cases.

parasar
08-25-2015, 09:47 PM
I still do not see any pre-Neolithic H1 or H3 among those samples listed above although I must admit that I do not know mtDNA haplogroup mutations very well. I do see a pre-Neolithic H6 and H though. Indeed some H probably was present in Europe before the neolithic but a lot also came to Europe with Neolithic farmers from Anatolia/Near East I think. Like I said before we need to look at SUBCLADES not just ''H''!...Look at mtDNA haplogroup U. Only certain subclades existed in UP and Mesolithic Europe. Those subclades are U5, U4 and U2. Other U subclades such as U1, U3 and K came later with Neolithic farmers or even later than that in some cases.

H1 and H3 both show star-like distributions which means that they expanded pretty rapidly. Which also indicates that prior to their expansion they were not widespread.

Perhaps this is outdated:
"The two most frequent sub-haplogroups, H1 and H3, each show a rather star-like phylogeny. ...
H1 is almost exclusively European, with its only incursion into the Near East being a few Palestinian individuals bearing the most common haplotype. ...
H3 is exclusively European, with no Near Eastern representatives...
The paraphyletic ancestral cluster, H*, is the main Near Eastern representative of haplogroup H, in agreement with the suggestion that the haplogroup evolved in the Near East and spread subsequently into Europe...
phylogeographic patterns displayed by sub-haplogroups H1 and H3 both closely resemble that of haplogroup V ...
The star-like phylogenies, geographic distribution, and estimated ages of all three clades suggest that they all took part in a major expansion from southwest to northeast Europe ∼12,000–14,000 years ago."
http://genome.cshlp.org/content/15/1/19.full

Humanist
08-25-2015, 09:55 PM
H1 and H3 both show star-like distributions which means that they expanded pretty rapidly. Which also indicates that prior to their expansion they were not widespread.

Perhaps this is outdated:
"The two most frequent sub-haplogroups, H1 and H3, each show a rather star-like phylogeny. ...
H1 is almost exclusively European, with its only incursion into the Near East being a few Palestinian individuals bearing the most common haplotype. ...
H3 is exclusively European, with no Near Eastern representatives...

It is indeed outdated. Those bits are from a paper from 2005. H1 in the Near East is certainly not restricted to "a few Palestinian individuals bearing the most common haplotype." And H3 is in fact observed in the Near East. Even though there are relatively few Assyrian Christians tested (~100), both H1 and H3 have been observed.

EDIT: Checking the Armenian DNA Project and Kurdish DNA Blogspot, H1 is observed in both groups. H3 is not. It is possible that the H3 in Assyrians is a relatively recent introduction, given that it is not observed in the two aforementioned neighboring groups.

Krefter
08-25-2015, 10:48 PM
We'll see H1 Neolithic Anatolians soon.

J Man
08-25-2015, 10:53 PM
H1 and H3 both show star-like distributions which means that they expanded pretty rapidly. Which also indicates that prior to their expansion they were not widespread.

Perhaps this is outdated:
"The two most frequent sub-haplogroups, H1 and H3, each show a rather star-like phylogeny. ...
H1 is almost exclusively European, with its only incursion into the Near East being a few Palestinian individuals bearing the most common haplotype. ...
H3 is exclusively European, with no Near Eastern representatives...
The paraphyletic ancestral cluster, H*, is the main Near Eastern representative of haplogroup H, in agreement with the suggestion that the haplogroup evolved in the Near East and spread subsequently into Europe...
phylogeographic patterns displayed by sub-haplogroups H1 and H3 both closely resemble that of haplogroup V ...
The star-like phylogenies, geographic distribution, and estimated ages of all three clades suggest that they all took part in a major expansion from southwest to northeast Europe ∼12,000–14,000 years ago."
http://genome.cshlp.org/content/15/1/19.full

''H1 and H3 both show star-like distributions which means that they expanded pretty rapidly''.....Neolithic farmers are great candidates for that.

J Man
08-25-2015, 10:55 PM
We'll see H1 Neolithic Anatolians soon.

I am curious...What exactly makes you so certain about that?

Krefter
08-25-2015, 11:32 PM
''H1 and H3 both show star-like distributions which means that they expanded pretty rapidly''.....Neolithic farmers are great candidates for that.

Exactly!!

Krefter
08-25-2015, 11:37 PM
I am curious...What exactly makes you so certain about that?

I posted earlier that of Neolithic European farmers tested for a H1 SNP a high frequency have it. Their H1 came from the East Mediterranean/Anatolia. I'll be very surprised if out of 32 none have H1.

I expect their mtDNA will be mostly: K1a, HV0, H1, H3, T2, J1c, N1a1a. I won't be surprised to see U5/U4/W/X/T1a either.

Leeroy Jenkins
08-25-2015, 11:50 PM
I am curious...What exactly makes you so certain about that?

You may have missed this from a few weeks ago:

http://eurogenes.blogspot.com/2015/07/a-little-more-on-genome-wide-affinities.html


the mtDNA HVI and HVII region sequences (354 and 217 bp, respectively) of seven ancient samples collected from Cemialo Sirti (Batman) excavation site in the southeastern of Anatolia were successfully obtained. The mtDNA HPG compositions of these ancient human samples were determined. The mtDNA haplogroups of seven ancient individuals were assigned as H1z1, M1a, U2b1, H1a, HV, R2 and R6

It isn't exactly indisputable proof to back Krefter's claim, but it certainly isn't contrarian either.

Krefter
08-26-2015, 12:07 AM
You may have missed this from a few weeks ago:

http://eurogenes.blogspot.com/2015/07/a-little-more-on-genome-wide-affinities.html


Those are 2500 years old mtDNA samples though.

J Man
08-26-2015, 12:27 AM
I posted earlier that of Neolithic European farmers tested for a H1 SNP a high frequency have it. Their H1 came from the East Mediterranean/Anatolia. I'll be very surprised if out of 32 none have H1.

I expect their mtDNA will be mostly: K1a, HV0, H1, H3, T2, J1c, N1a1a. I won't be surprised to see U5/U4/W/X/T1a either.

What are your thoughts on the so called H1 samples from Mesolithic Portugal? Personally I think the study is not reliable since it is from 2005 and there is probably issues with contamination.

parasar
08-26-2015, 12:29 AM
''H1 and H3 both show star-like distributions which means that they expanded pretty rapidly''.....Neolithic farmers are great candidates for that.

For the expansion, yes. For origin, not necessarily.
I still think Iberia played a part. Or maybe NW Africa, as there is some connection of U6 with NW Africa too.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013378

Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000–9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x ...
Moroccans and Tunisians, the populations geographically closest to Europe, harbor the highest diversity values for all considered indices. Thus, the coastal areas of northwestern Africa, after the arrival of the Iberian founder H1 mtDNAs, probably acted as centers for the subsequent diffusion of H1 in the internal regions of North Africa.

http://www.biomedcentral.com/1471-2148/14/109

This continuity has received some support from ancient DNA studies on Iberomaurusian remains, with an age around 12 kya, exhumed from the archaeological site of Taforalt in Morocco [17]. In this analysis, haplotypes tentatively assignable to haplogroups H, JT, U6 and V were identified, pointing to a local evolution of this population and a genetic continuity in North Africa. On the other hand, only one haplotype harbored the 16223 mutation, which if assigned to an L haplogroup would represent a sub-Saharan African influence of about 4%. This would equate to a frequency five times lower than that found in current Moroccan populations (20%) and would support the proposal that the penetration of sub-Saharan mtDNA lineages to North Africa mainly occurred since the beginning of the Holocene onwards


Those are 2500 years old mtDNA samples though.

Plus we have M1 and U2b1 in the mix.

J Man
08-26-2015, 12:30 AM
For the expansion, yes. For origin, not necessarily.
I still think Iberia played a part. Or maybe NW Africa, as there is some connection of U6 with NW Africa too.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013378

http://www.biomedcentral.com/1471-2148/14/109




Plus we have M1 and U2b1 in the mix.

There is also some U5b present in North Africa. Anyway more testing of ancient remains will tell us what the case for H1 and H3 truly is in time.

Krefter
08-26-2015, 12:59 AM
]http://www.biomedcentral.com/1471-2148/14/109[/url]


It was just HVR1 coverage. The rCRS would be H, the JTs looked like branches of R0a. There are many possibilities. And who knows if the samples weren't contaminated anyways.


What are your thoughts on the so called H1 samples from Mesolithic Portugal? Personally I think the study is not reliable since it is from 2005 and there is probably issues with contamination.

I think they're mostly false results. Neolithic samples from the same study didn't make any sense(Many were R*) and the H1b1a-h haplotype was shared between Mesolithic and Neolithic, as if they had a common contamination source. H1b1a-h is very rare. Under 1% have it today.

parasar
08-26-2015, 01:16 AM
It was just HVR1 coverage. The rCRS would be H, the JTs looked like branches of R0a. There are many possibilities. And who knows if the samples weren't contaminated anyways.



I think they're mostly false results. Neolithic samples from the same study didn't make any sense(Many were R*) and the H1b1a-h haplotype was shared between Mesolithic and Neolithic, as if they had a common contamination source. H1b1a-h is very rare. Under 1% have it today.

What is the evidence of contamination? Plus lot of mtDNA phylogeny is based on HVR1 markers, with haplogroups defined by them.

Google translated:
http://secher.bernard.free.fr/blog/index.php?post/2015/04/03/ADN-mitochondrial-ancien-en-Cantabrie-dans-le-nord-de-l-Espagne

One sample is new in this study: a Magadalénien skeleton of a woman of El Miron Cave in Cantabria. HVR1 and HVR2 control areas have been tested and the main markers of the coding region by RFLP for discriminating haplogroups. Among these samples, 5 were hunter-gatherers Magdalenians or Mesolithic (.. 16,700 BC) El Miron , Errala (11,000 BC..), La Pasiega, La Hora (5350 BC..) and Aizpea (5550 BC..).
The results of hunter-gatherers give 3 samples of haplogroup H and 2 samples of haplogroup U

Krefter
08-26-2015, 03:23 AM
What is the evidence of contamination? Plus lot of mtDNA phylogeny is based on HVR1 markers, with haplogroups defined by them.


For the Ancient North Africans: There are many possible haplogroups based on the HV1 data. I looked at it once and the JTs are based on 16126C which is fairly popular. In terms of the Iberians, I know they tested CR SNPs and they're H. I think it is possible they're contaminated. Either way the chances of much of modern European H being of pre-Neolithic origin is low.

speedyran
08-26-2015, 07:26 AM
Though I am not sure if Kalash and Bored lineage is Eurasian, but lot many Indians have the U maternal lineage, generally, it is not the same as the European one, only very distantly related to it. I had also posted mine here earlier but then realized that he was not interested in the West Asian but West Eurasian, I had misread the title, so I deleted it.

Also mtDNA mutates much slower than the yDNA, thus is not of great importance in genealogy, again most cultures are patrilineage thus are interested in the yDNA more than the mtDNA.

I hardly knew anything about Kalash. Following on from some posts in this forum, I did read up on them a bit. Apparently they differ from others in south Asia by having no south Asian maternal lines. All their maternal lines are said to be West Eurasian. I think they have 34% U4 mtDNA. Presumably then their U4 is West Eurasian. Paternally they are said to be mainly similar to other south Asians. TBH I can't understand all this stuff fully but I am now able to follow it somewhat better.

paulgill
08-26-2015, 08:17 AM
I hardly knew anything about Kalash. Following on from some posts in this forum, I did read up on them a bit. Apparently they differ from others in south Asia by having no south Asian maternal lines. All their maternal lines are said to be West Eurasian. I think they have 34% U4 mtDNA. Presumably then their U4 is West Eurasian. Paternally they are said to be mainly similar to other south Asians. TBH I can't understand all this stuff fully but I am now able to follow it somewhat better.

I don't know much about their maternal lines, they are one of the old isolated populations in that area who refused to mixed up with the surrounding populations and follow their own ancient culture and religions. They are perhaps more Yamnaya like population and some think they were originally from caucasus. Parasar, Kurd and other on the other threads know better about them. Trouble with the haplogroups is that most are found all over the world now, but where they or their particular subclads originated is difficult to determine, that requires the time of a particular mutation, and then the ancient samples from that time frame as evidence, to establish a certain location as the place of its origin, not easy I guess.

As in my case, my paternal line is thought to have originated in Eastern Anatolia, but I am one of very lucky ones, as we still use the name of Khabur river in that area as surname and also sometimes name our towns so too. And my maternal line been found in an ancient 4800+yrs old sample from Syrian Sumeria, so basically both of my lines are from the Khabur River Triangle. But my maternal haplogroup is found in much of Europe, Caucasus, Iran, Anatolia, Syria, Iraq, SCAsia, Pakistan and a little bit in NW India also.

bored
08-26-2015, 08:36 AM
I hardly knew anything about Kalash. Following on from some posts in this forum, I did read up on them a bit. Apparently they differ from others in south Asia by having no south Asian maternal lines. All their maternal lines are said to be West Eurasian. I think they have 34% U4 mtDNA. Presumably then their U4 is West Eurasian. Paternally they are said to be mainly similar to other south Asians. TBH I can't understand all this stuff fully but I am now able to follow it somewhat better.

Yes, U4b is West Eurasian. There's no debate about that. It's well established.

Sapporo
08-26-2015, 09:42 AM
I hardly knew anything about Kalash. Following on from some posts in this forum, I did read up on them a bit. Apparently they differ from others in south Asia by having no south Asian maternal lines. All their maternal lines are said to be West Eurasian. I think they have 34% U4 mtDNA. Presumably then their U4 is West Eurasian. Paternally they are said to be mainly similar to other south Asians. TBH I can't understand all this stuff fully but I am now able to follow it somewhat better.

I am presuming you read that on wiki as quoted below. That is what it states. Not sure if no M maternal lines exist among Kalash but they have a high rate of indigenous Y-DNA with H1 at 20.5%.



Genetic analysis of Y-chromosome DNA (Y-DNA) by Firasat et al. (2007) on Kalash individuals found high and diverse frequencies of these Y-DNA Haplogroups: L3a (22.7%), H1* (20.5%), R1a (18.2%), G (18.2%), J2 (9.1%), R* (6.8%), R1* (2.3%), and L* (2.3%).[38]

Genetic analysis of Mitochondrial DNA (mtDNA) by Quintana-Murci et al. (2004) stated that "the western Eurasian presence in the Kalash population reaches a frequency of 100%" with the most prevalent mtDNA Haplogroups being U4 (34%), R0 (23%), U2e (16%), and J2 (9%). The study asserted that no East or South Asian lineages were detected and that the Kalash population is composed of western Eurasian lineages (as the associated lineages are rare or absent in the surrounding populations). The authors concluded that a western Eurasian origin for the Kalash is likely, in view of their maternal lineages

bored
08-26-2015, 10:13 AM
I am presuming you read that on wiki as quoted below. That is what it states. Not sure if no M maternal lines exist among Kalash but they have a high rate of indigenous Y-DNA with H1 at 20.5%.

Damn that's a high rate of indigenous Y-DNA indeed.

Coldmountains
08-26-2015, 10:30 AM
I don't know much about their maternal lines, they are one of the old isolated populations in that area who refused to mixed up with the surrounding populations and follow their own ancient culture and religions. They are perhaps more Yamnaya like population and some think they were originally from caucasus. Parasar, Kurd and other on the other threads know better about them. Trouble with the haplogroups is that most are found all over the world now, but where they or their particular subclads originated is difficult to determine, that requires the time of a particular mutation, and then the ancient samples from that time frame as evidence, to establish a certain location as the place of its origin, not easy I guess.

As in my case, my paternal line is thought to have originated in Eastern Anatolia, but I am one of very lucky ones, as we still use the name of Khabur river in that area as surname and also sometimes name the town so too. And my maternal line been found in an ancient 4800+yrs old sample from Syrian Sumeria, so basically both of my lines are from the Khabur River Triangle. But my maternal haplogroup is found in much of Europe, Caucasus, Iran, Anatolia, Syria, Iraq, SCAsia, Pakistan and a little bit in NW India also.

Ironically Kalash seem to have the lowest percentages of R1a1a among South Central Asian and North South Asian populations. I don't know what this means in the end but I still have my doubts about their so high direct steppe admixture based on their low R1a (20%). They are also extremely low in any WHG unlike some Pamiri Tajiks and Jatts and are also lower in it than Pashtuns. Much of their steppe-like looking admixture or mtdna can be just shared teal/ANE stuff of pre-IE origin. But it is also possible that much of their WHG is not showing in calculators according to some models Davidski presented. Their low R1a1a could also originate from other reasons like bottle necks, founder effects, less strict patriarchy ...

bored
08-26-2015, 10:52 AM
^^
In addition, I'm surprised that Kalash have such a high frequency of indigenous Y-DNA.

Sapporo
08-26-2015, 11:09 AM
Damn that's a high rate of indigenous Y-DNA indeed.

L3a (22.7%), a distantly related subclade of L3* (L1c-M357)? is also found at a very high rate among them and also found among Pamiri Tajiks, certain Durrani Pashtuns and certain Jatt groups and other NW South Asian populations. It's also found at lower rates throughout the subcontinent. Although, L1 is much more common. I speculate that L3 is indigenous to South Central Asia/Indus Valley give its frequency in the Northwestern corridor and much less elsewhere. This is all guesswork of course.

Krefter
08-26-2015, 01:27 PM
I hardly knew anything about Kalash. Following on from some posts in this forum, I did read up on them a bit. Apparently they differ from others in south Asia by having no south Asian maternal lines. All their maternal lines are said to be West Eurasian. I think they have 34% U4 mtDNA. Presumably then their U4 is West Eurasian. Paternally they are said to be mainly similar to other south Asians. TBH I can't understand all this stuff fully but I am now able to follow it somewhat better.

It's a small sample set of 40 or so Kalash. You can find the data on my Blog(On the Right it says, "Link to all my mtDNA data"). The high amount of U4 is the result of founder effects. They probably do have South Asian lineages, just several western ones became popular because of founder effects(That's what happens in small isolated populations).

parasar
08-26-2015, 03:50 PM
It's a small sample set of 40 or so Kalash. You can find the data on my Blog(On the Right it says, "Link to all my mtDNA data"). The high amount of U4 is the result of founder effects. They probably do have South Asian lineages, just several western ones became popular because of founder effects(That's what happens in small isolated populations).

I would agree on the founder effect.

It is possible that the isolated Kalash harbor mtDNA types that were at one time much more common in that part of South Asia. I would ascribe to their U4b an Altain connection. I think U4/U4b moved west with C/C4a in the pre/Neolithic period.

As far as U4 overall in India is concerned, it is in low %ages but is present all over:
"Kivisild et al. (1999) studied 550 Indian mtDNA
samples, chiefly obtained from Uttar Pradesh
(Tharu, Buksa, Mixed castes), Punjab (Lobana)
and Andhra Pradesh (Lambadi, Mixed castes),
by sequencing hypervariable region I (HVI) and
by performing RFLP analysis. Among the
observed haplogroups, U was found to be the
second most prevalent haplogroup (~ 13%) in
India, being more common (~ 23%) in north India
(Uttar Pradesh, n = 103) than in south India, ~
10% (Andhra Pradesh, n = 250). The principal
sub-haplogroup of U in India is U2 (named U2i),
which lacks a characteristic transversion at np
16129 and hence differs from the WesternEurasian
variety of U2 (named U2e). In India, U2i
exhibited a frequency of about 78% of the total,
U followed by U7 that showed a frequency of
about 13%. The split between Indian and
Western-Eurasian U2 lineages was estimated to
be 53,000 ± 4,000 ybp and the coalescence age of
U7 was calculated to be 32,000 ± 5,500 years.
Other subclusters of U found at lower frequencies
were U1 (2.3%), U4 (4.7%), U5 (1.2%) and K
(1.2%)"
"Barnabas et al. (2005) reported four
sub-haplogroups of U: U1, U2i U4, and U7a, in
his study consisting of 117 Indians ... U4 was exclusively
present among the Telegu speakers of Andhra
Pradesh"
Kashyap (2005) observed U2i, U2a, U2b, U2c,
U3, U4, U5a1a, U7 and K sub-haplogroups of U
in their study on Desasth Brahmins (n = 19),
Chitpavan Brahmin (n= 20), Dhangar (n=19) and
Maratha (n= 19) populations of Maharashtra ...
Dhangars showed U2i, U2a, U2c, U4, U7 and K"

Krefter
08-26-2015, 09:36 PM
Just added 1700 samples from Ireland, Scotland, Estonia, Seto(Minority in Estonia), Lithuania, Latvia, Russia, Karelia, Finland, Saami, Vespian, and more, to use in my next post. Just need to get more samples from France, Central Europe, Caucasus, Iraq, and Afghanistan to get dense coverage of all of West Eurasia.

My next post should be ready next week or a little later.

After I'm done with my West Eurasia posts. I'm going to look into Siberia, Central Asia, China, SouthEast East Asia, and the Americas. I'll compare them to each other and West Eurasians.

paulgill
08-26-2015, 10:08 PM
^^
In addition, I'm surprised that Kalash have such a high frequency of indigenous Y-DNA.

Different culture, women have freedom to choose their partner and that I think is the reason for that high H1, etc.

Ebizur
08-26-2015, 10:15 PM
I would agree on the founder effect.

It is possible that the isolated Kalash harbor mtDNA types that were at one time much more common in that part of South Asia. I would ascribe to their U4b an Altain connection. I think U4/U4b moved west with C/C4a in the pre/Neolithic period.The U4b individual in the HGDP Kalash sample (HGDP00290) is more precisely a Kalash male who belongs to mtDNA haplogroup U4b1a4 and Y-DNA haplogroup G2a. I recall reading on Eupedia that U4b1a4 also has been found in a sample of Tubalars (Turkic speakers in the Altai Mountains). It is possible that this Kalash U4b1a4 individual's direct matrilineal ancestor may have come to Chitral from Altai, but it is also possible that the ancestors of both the Kalash U4b1a4 and the Tubalar U4b1a4 have arrived at their present locations from elsewhere.

In any case, the more common form of U4 among the Kalash is U4a1, which has experienced a major founder effect. Though at least two branches of U4a1 have been found among the Kalash, only one of those branches is responsible for the founder effect among them that has elevated the frequency of U4a to its regional (and perhaps worldwide) maximum.

paulgill
08-26-2015, 10:58 PM
It was just HVR1 coverage. The rCRS would be H, the JTs looked like branches of R0a. There are many possibilities. And who knows if the samples weren't contaminated anyways.



I think they're mostly false results. Neolithic samples from the same study didn't make any sense(Many were R*) and the H1b1a-h haplotype was shared between Mesolithic and Neolithic, as if they had a common contamination source. H1b1a-h is very rare. Under 1% have it today.


Do you understand if H1b1a-h is very rare then the chances of contamination are also near nil?

paulgill
08-26-2015, 11:15 PM
It was just HVR1 coverage. The rCRS would be H, the JTs looked like branches of R0a. There are many possibilities. And who knows if the samples weren't contaminated anyways.



I think they're mostly false results. Neolithic samples from the same study didn't make any sense(Many were R*) and the H1b1a-h haplotype was shared between Mesolithic and Neolithic, as if they had a common contamination source. H1b1a-h is very rare. Under 1% have it today.

L-M357, I think, is Elamite, Iranic tribes, Jatts of that origin are L-M357. J2 and G are IVC etc.


L3a (22.7%), a distantly related subclade of L3* (L1c-M357)? is also found at a very high rate among them and also found among Pamiri Tajiks, certain Durrani Pashtuns and certain Jatt groups and other NW South Asian populations. It's also found at lower rates throughout the subcontinent. Although, L1 is much more common. I speculate that L3 is indigenous to South Central Asia/Indus Valley give its frequency in the Northwestern corridor and much less elsewhere. This is all guesswork of course.

paulgill
08-26-2015, 11:23 PM
It's a small sample set of 40 or so Kalash. You can find the data on my Blog(On the Right it says, "Link to all my mtDNA data"). The high amount of U4 is the result of founder effects. They probably do have South Asian lineages, just several western ones became popular because of founder effects(That's what happens in small isolated populations).

Agreed, but total Kalash population is very small and their auDNA is also a bit different than average SAsian.

J Man
08-27-2015, 12:19 PM
To me it is very obvious now that mtDNA haplogroups U5a, U5b, U4 and U2e are the main if not the only true WHG and EHG mtDNA lineages. U5a, U4 and U2e seem to correlate strongly with the EHG population(s) while U5b seems to correlate strongly with the WHG population(s). Obviously though there was some mixture over time between WHG and EHG groups in parts of Central, Eastern and Northern Europe during the Mesolithic.

J Man
08-27-2015, 12:42 PM
For the Ancient North Africans: There are many possible haplogroups based on the HV1 data. I looked at it once and the JTs are based on 16126C which is fairly popular. In terms of the Iberians, I know they tested CR SNPs and they're H. I think it is possible they're contaminated. Either way the chances of much of modern European H being of pre-Neolithic origin is low.

Exactly which mtDNA haplogroups that are present among Europeans today do you think came to Europe during the Neolithic as farmers from Anatolia/East Mediterranean?

Kale
08-27-2015, 12:48 PM
Do you understand if H1b1a-h is very rare then the chances of contamination are also near nil?

If 1 in 100 people have that haplogroup, and it was found twice (across a long stretch of time) that's a 1 in 10,000 chance. Presuming a researcher had that haplogroup, and there was more greater than a 1 in 100 chance of contamination, than contamination is still more likely.

Krefter
08-29-2015, 04:29 AM
Just looked at some stats on H-subclade percentages in West Asia and Europe. H1 is usually 1% in West Asia and 10%+ in Europe. I'll post about H-diversity and info on full-sequenced mtDNA in my "Part 3: Looking for mtDNA diversity in West Eurasia".

J Man
08-30-2015, 04:30 AM
Just looked at some stats on H-subclade percentages in West Asia and Europe. H1 is usually 1% in West Asia and 10%+ in Europe. I'll post about H-diversity and info on full-sequenced mtDNA in my "Part 3: Looking for mtDNA diversity in West Eurasia".

Exactly which mtDNA haplogroups that are present among Europeans today do you think came to Europe during the Neolithic as farmers from Anatolia/East Mediterranean?

Krefter
08-31-2015, 04:12 AM
Exactly which mtDNA haplogroups that are present among Europeans today do you think came to Europe during the Neolithic as farmers from Anatolia/East Mediterranean?

Nothing has changed in my mind recently because I haven't looked at high-coverage data yet. Definitly JT, U1, U3, K, N1, N2, and X. Then um most H and probably HV0. But there's plenty of room for some subclades in those haplogroups to be of even Upper Palaeolithic origin. But it seems most non-U5/U4/U2e came in the Neolithic to me.

J Man
08-31-2015, 03:45 PM
Nothing has changed in my mind recently because I haven't looked at high-coverage data yet. Definitly JT, U1, U3, K, N1, N2, and X. Then um most H and probably HV0. But there's plenty of room for some subclades in those haplogroups to be of even Upper Palaeolithic origin. But it seems most non-U5/U4/U2e came in the Neolithic to me.

Okay you mention JT. Do you think then that all mtDNA haplogrup J and all of it's subclades came to Europe initially with Neolithic farmers from Anatolia/Near East or in some cases even a bit later? Same with mtDNA haplogroup T and all of it's subclades?

J Man
09-02-2015, 07:30 PM
Nothing has changed in my mind recently because I haven't looked at high-coverage data yet. Definitly JT, U1, U3, K, N1, N2, and X. Then um most H and probably HV0. But there's plenty of room for some subclades in those haplogroups to be of even Upper Palaeolithic origin. But it seems most non-U5/U4/U2e came in the Neolithic to me.

Okay you mention JT. Do you think then that all mtDNA haplogrup J and all of it's subclades came to Europe initially with Neolithic farmers from Anatolia/Near East or in some cases even a bit later? Same with mtDNA haplogroup T and all of it's subclades?

Krefter
09-02-2015, 09:15 PM
Okay you mention JT. Do you think then that all mtDNA haplogrup J and all of it's subclades came to Europe initially with Neolithic farmers from Anatolia/Near East or in some cases even a bit later? Same with mtDNA haplogroup T and all of it's subclades?

Some could have been there before the Neolithic and some came later after the Neolithic. J1c/T2b looks like EEF, J1b1a1/J2b1a/J2a1a/T1a/T2a look like Steppe, and J1b(xJ1b1a)/J1d/T1a look West Asian.

Krefter
09-02-2015, 11:22 PM
U8c in Poland and Upper Palaeolithic Czech Republic: I'm doing analysis for my second post and realized one of the Us from Poland could be U8c. U8c has not been reported in any modern people as far as I know. It is a fully-sequenced mtDNA sample from Upper Palaeolithic Czech Republic that is around 30,000 years old and was a brother of the popular clade U8b(K is U8b2). Two U5*s(negative for U5a'b) were found in the same site with U8c.

Most U8 falls under U8a1a, U8b2(K), and U8b1. There's prove U8 has been around for 30,000 years. U8b2(K) probably evolved in UHGs in West Asia but there's no way to know for sure, and we know U8c an uncle to U8b2(K) was in Europe 30,000 years ago. U8a1a, U8b1, and some U8b2(K) might have unique and old-histories in multiple regions.

J Man
09-03-2015, 12:12 AM
Some could have been there before the Neolithic and some came later after the Neolithic. J1c/T2b looks like EEF, J1b1a1/J2b1a/J2a1a/T1a/T2a look like Steppe, and J1b(xJ1b1a)/J1d/T1a look West Asian.

Haplogroups J1b1a1/J2b1a/J2a1a/T1a/T2a that you say look like Steppe mtDNA lineages probably have their roots in the Neolithic farming groups of Anatolia/West Asia before they spread into the Steppe though eh?

Krefter
09-03-2015, 02:10 AM
Haplogroups J1b1a1/J2b1a/J2a1a/T1a/T2a that you say look like Steppe mtDNA lineages probably have their roots in the Neolithic farming groups of Anatolia/West Asia before they spread into the Steppe though eh?

Yeah, I tend towards that origin. T1a is fairly popular in West Asia and J1b(xJ1b1a1) is very popular. But who knows some could be EHG. Remember the T from hunter gatherers in Karelia?

J Man
09-03-2015, 01:55 PM
Yeah, I tend towards that origin. T1a is fairly popular in West Asia and J1b(xJ1b1a1) is very popular. But who knows some could be EHG. Remember the T from hunter gatherers in Karelia?

That T sample from the Karelian hunter-gatherers comes from a relatively later time period though (3500 BP) so it could come from admixture with Neolithic groups from further South. Hard to say though I suppose at this point.

J Man
09-03-2015, 03:43 PM
A good amount of H has shown up among the Neolithic Cardial Ware samples from the new Inigo study. Here are the results of 6 newly tested Cardial samples.

http://mbe.oxfordjournals.org/content/suppl/2015/09/02/msv181.DC1/cardial_supplementary_MBE_submission.pdf

K1a2a
X2c
H4a1a
H3
H4a1a
K1a4a1

Krefter
09-03-2015, 04:12 PM
A good amount of H has shown up among the Neolithic Cardial Ware samples from the new Inigo study. Here are the results of 6 newly tested Cardial samples.

http://mbe.oxfordjournals.org/content/suppl/2015/09/02/msv181.DC1/cardial_supplementary_MBE_submission.pdf

K1a2a
X2c
H4a1a
H3
H4a1a
K1a4a1

All expected. All of them were tested at high coverage unlike my modern samples. But among my high-coverage samples all those clades are very typical today except X2c. X2b is the main type of X.

J Man
09-03-2015, 06:55 PM
All expected. All of them were tested at high coverage unlike my modern samples. But among my high-coverage samples all those clades are very typical today except X2c. X2b is the main type of X.

More evidence that H3 is a Neolithic farmer lineage that originated in Anatolia/Near East. Where is H4a1a most common today? Europe?

Krefter
09-05-2015, 06:39 AM
I'm working on Part 2: Looking for mtDNA Diversity in West Eurasia: I'm putting focusing on finding diversity in H because it is popular and the most undefined. Important to understand: Sardinia shows similar frequency of H1 as most of Europe, and similar H3 to Iberia and British Isles(Balts, Finns, Swedes have little H3). Over 50% of their H is H1 and H3. About 50% of Sardinian Y DNA if EEF/WHG(I2a1+G2a), and considering how EEF-like they're autosomally most of their mtDNA should be EEF/WHG.

avalon
09-05-2015, 07:47 AM
I'm working on Part 2: Looking for mtDNA Diversity in West Eurasia: I'm putting focusing on finding diversity in H because it is popular and the most undefined. Important to understand: Sardinia shows similar frequency of H1 as most of Europe, and similar H3 to Iberia and British Isles(Balts, Finns, Swedes have little H3). Over 50% of their H is H1 and H3. About 50% of Sardinian Y DNA if EEF/WHG(I2a1+G2a), and considering how EEF-like they're autosomally most of their mtDNA should be EEF/WHG.

Do you have much of a breakdown of mtDNA H subclades in the British Isles? According to the eupedia maps the frequencies of H1 and H3 look quite high in the Isles. So I guess a key question would be - how much of this is derived from Neolithic Britons and how much is derived from Bronze Age immigrants such as Bell Beaker?

Krefter
09-05-2015, 09:17 AM
Do you have much of a breakdown of mtDNA H subclades in the British Isles? According to the eupedia maps the frequencies of H1 and H3 look quite high in the Isles. So I guess a key question would be - how much of this is derived from Neolithic Britons and how much is derived from Bronze Age immigrants such as Bell Beaker?

British isles are in line with the rest of Europe. Their H3 is high like Iberia and unlike Sweden+Baltic region.

J Man
09-15-2015, 01:42 AM
British isles are in line with the rest of Europe. Their H3 is high like Iberia and unlike Sweden+Baltic region.

I will not ask this again until the ancient DNA results from the Anatolian Neolithic farmers are in but I want to ask you one more time. I am sorry and I hope I am not bothering you to much about this. Exactly which mtDNA haplogroups do you think were present among and spread into Europe with Anatolian neolithic farmers? Can you list them please?

Krefter
09-15-2015, 03:30 AM
I will not ask this again until the ancient DNA results from the Anatolian Neolithic farmers are in but I want to ask you one more time. I am sorry and I hope I am not bothering you to much about this. Exactly which mtDNA haplogroups do you think were present among and spread into Europe with Anatolian neolithic farmers? Can you list them please?

I'm not bothered by questions don't worry about it. Ancient mtDNA makes it clear: K1a, J1c, T2b, T2c1, T2e, HV0, H1, H3, H5, N1a1a, X2a-o, W1 took up the majority of their mtDNA. Of course they also belonged to other forms of U(xK), K, J, T, H, X, and W.

Krefter
09-16-2015, 08:04 PM
@Everyone,

Looking at some high-coverage data, I think we can start identifying specific lineages that are mostly of "Steppe" origin: U5a1a1, U5a1b, U5a1d2, U5a1c, U4b1a1, J1b1a1, H6a1, H2a2, H2a1, T1a1 are nine suspects. Once I find more high-coverage data more will appear.

alan
09-16-2015, 09:41 PM
Here. Sorry it is messy, I was editing it today and did not finish.

https://docs.google.com/spreadsheets/d/1HcAhe7QvggT792VruuoZX6IsTg4LhWXV-Z_ZfTk2KGA/edit#gid=1405879894

Of Neolithic H samples tested for an H1 and H3 SNP.

3/10 H1 from LBK
10/20 have H1 and 4/20 have H3 from Early Neolithic France
3/6 have H1 and 3/6 have H3 from Middle Neolithic France.
2/4 have H3 and 1/4 have H1 from Middle Neolithic Central Europe.
1/1 have H1 from Megalithic Spain.

But from Yamnaya/Catacomb.
2/19 are H1 and 0/19 are H3.

Your doing a useful but of work there.

Krefter
09-20-2015, 10:35 PM
I found study which fully-sequenced 352 Iranian mtDNAs. I just finished adding Persian results. Of 29 Hs, 30% are basal forms of H not found in fully-sequenced Basque and Danish. 14% are not classified by phlotree. 100% of Danish and 98% of Basque H is classifed by phylotree. All of their H1s are unclassified by phylotree.

Describition of relationship between fully-sequenced Persian and European(Basque, Danish) H. Note that even the green-colored ones probably separated many 1,000s of years ago, it;'s just those haplogroups haven't been studied enough and their subclades haven't been identified.

All Separated 8,000+ years ago.
All but a few separated 8,000+ years ago.
Most Separated 8,000+ years ago. Some have close relation
Most are of the same(for as far as phylo classifies them)

Classified Persian H is: H13a2=5, H1=5, H14b=2, H5=3, H3=2, H57=2, H66=1, H63=1, H7b=1, H10=1, H15=1.

As you can see Persian H and European H are very differnt. In U, J, T, R0(xH), N(xR), and X(?, not enough samples) the differences between West Asia and Europe are much greater. In W and N1a1b2(aka I) there seems to be more sharing. Basically it looks like almost 100% of West Asian and European maternal lineages split from each other in the Neolithic or earlier. This is consistent with autosomal DNA. West Eurasian mtDNA diversity is defined mostly in a West Asia vs Europe axis. With low coverage testing it is nearly impossible to differentiate most Europeans from each other and the same is true for West Asians.

DMXX
09-21-2015, 09:53 PM
Good work Krefter. Your conclusions are in line with some of the statistics produced by older papers regarding the correlation with geography and uniparental markers. mtDNA tends to be more geography-associated than Y-DNA.

I would have swallowed my laptop whole anaconda-style if you found Persian and European mtDNA H had significant overlap.

Krefter
09-21-2015, 11:25 PM
I would have swallowed my laptop whole anaconda-style if you found Persian and European mtDNA H had significant overlap.

https://imgflip.com/readImage?iid=9422987

Humanist
09-21-2015, 11:46 PM
Was just taking a look at your mtDNA frequencies. Correct me if I am wrong, but you are not breaking up country frequencies by ethnic groups, correct? In some (all?) ME countries, haplogroup frequencies can differ significantly between ethnic groups.

Krefter
09-21-2015, 11:57 PM
Was just taking a look at your mtDNA frequencies. Correct me if I am wrong, but you are not breaking up country frequencies by ethnic groups, correct? In some (all?) ME countries, haplogroup frequencies can differ significantly between ethnic groups.

Ethnic origin wasn't given for any of my samples, except for in Afghanistan, India, and Russia. In the other studies they confirmed the maternal line had been in their country for as long the records go. Immigrants, etc. were not tested of course.

Krefter
09-24-2015, 02:13 PM
A common U5b haplotype is U5b-16189!-16192!. It appears to be most popular in NorthEast Europe. Three U5b subclades have this haplotype, although from data I've seen so far usually they are U5b1. Two U5b1 subclades have this haplotype: U5b1e'h and U5b1b1a'd'f. A popular subclade of U5b1b1a'd'f is U5b1b1a, which appears to be most popular in NorthEast Europe but also has a presence in the Balkans and Scandinavia. U5b-16189!-16192! has been found in two Mesolithic Northern Poland samples, dating about 6,000 years old. There's a good chance they had U5b1b1a'd'f.

If NorthEast European U5b is tested at high coverage I'm confident a large amount will be U5b1b1a'd'f and it'll be very diverse. I suspect U5b1b1a'd'f originated Neolithic/Mesolithic lineage in NorthEast Europe.

Krefter
09-29-2015, 09:29 PM
There are many U4 samples from European hunter gatherers, but a small amount have been able of ind their subclade because of low coverage. Three U4 lineages have been found in Mesolithic East Europe: U4d*, U4b1, and U4a1.

U4d*: It has been found in several fully-sequenced mtDNAs from Pitted Ware in Gotland. It was a founder effect-lineage. Most PWC hunter gatherers belonged to a now dead or very rare U4d lineage. Two 7000 year old and one 7500 year old U4 from Karelia are HVR1 match with most U4s from PWC Gotland. This could mean they also had U4d*, and that there was a U4d clade popular in far Northern Europe in the Mesolithic that is rare or extinct today.

U4b1, U4b1a1a1: Was found in a 7000 year old Mesolithic forager in an Island next to Sweden. U4b1 is one of the major U4 clades today. HVR1, HVR2, and CR data for this sample wasn't given. It may have been U4b1* making it a likely dead or rare lineage today. A U4 with extra mutation 16362, which defines U4b1a1a1, has been found in Mesolithic Siberia. U4b1a1a1 isn't popular but exists today, and has been found in Corded Ware.

U4a1: U4a1 is a popular clade of U4 today, maybe the most popular. It has been found in Pitted Ware Gotland dating around 4800 BP and Karelia dating 3500 BP. The Karelian U4a1s had extra mutations 16093 and 16129. U4a1s with these extra mutations have been found in modern Karelia, Volga Ural Russia, and Norway. This tells us this U4a1 lineage survived well and that U4a1 in general survived well, probably expanding with IE-speaking groups from East Europe in the Bronze age. U4a1 has been Yamnaya, Sintashta/Andronovo, Corded Ware, Bell Beaker, and Unetice.

My general impression on U4 is that it's mostly an EHG lineage. It looks like it evolved in East Europe for 10,000s of years. Pitted Ware's U4d* is a dead lineage but that's because Pitted Ware is a dead cousin not an ancestor. U4 probably mostly expanded with Steppe-groups. It peaks in Volga/Ural at almost 10%, then in Balts at about 5%, then other East Europeans at 3-4%, and NW Europeans at 2-3%. U5a and U4 correlate very well with EHG and Steppe ancestry.

J Man
10-07-2015, 02:36 AM
There are many U4 samples from European hunter gatherers, but a small amount have been able of ind their subclade because of low coverage. Three U4 lineages have been found in Mesolithic East Europe: U4d*, U4b1, and U4a1.

U4d*: It has been found in several fully-sequenced mtDNAs from Pitted Ware in Gotland. It was a founder effect-lineage. Most PWC hunter gatherers belonged to a now dead or very rare U4d lineage. Two 7000 year old and one 7500 year old U4 from Karelia are HVR1 match with most U4s from PWC Gotland. This could mean they also had U4d*, and that there was a U4d clade popular in far Northern Europe in the Mesolithic that is rare or extinct today.

U4b1, U4b1a1a1: Was found in a 7000 year old Mesolithic forager in an Island next to Sweden. U4b1 is one of the major U4 clades today. HVR1, HVR2, and CR data for this sample wasn't given. It may have been U4b1* making it a likely dead or rare lineage today. A U4 with extra mutation 16362, which defines U4b1a1a1, has been found in Mesolithic Siberia. U4b1a1a1 isn't popular but exists today, and has been found in Corded Ware.

U4a1: U4a1 is a popular clade of U4 today, maybe the most popular. It has been found in Pitted Ware Gotland dating around 4800 BP and Karelia dating 3500 BP. The Karelian U4a1s had extra mutations 16093 and 16129. U4a1s with these extra mutations have been found in modern Karelia, Volga Ural Russia, and Norway. This tells us this U4a1 lineage survived well and that U4a1 in general survived well, probably expanding with IE-speaking groups from East Europe in the Bronze age. U4a1 has been Yamnaya, Sintashta/Andronovo, Corded Ware, Bell Beaker, and Unetice.

My general impression on U4 is that it's mostly an EHG lineage. It looks like it evolved in East Europe for 10,000s of years. Pitted Ware's U4d* is a dead lineage but that's because Pitted Ware is a dead cousin not an ancestor. U4 probably mostly expanded with Steppe-groups. It peaks in Volga/Ural at almost 10%, then in Balts at about 5%, then other East Europeans at 3-4%, and NW Europeans at 2-3%. U5a and U4 correlate very well with EHG and Steppe ancestry.


You have probably already seen this but just in case you did not yet.

http://www.researchgate.net/publication/273127695_When_hunter-gatherers_became_farmers_perspectives_from_a_late_ Danubian_Neolithic_site_in_Central_Poland

Krefter
10-07-2015, 03:36 AM
You have probably already seen this but just in case you did not yet.

http://www.researchgate.net/publication/273127695_When_hunter-gatherers_became_farmers_perspectives_from_a_late_ Danubian_Neolithic_site_in_Central_Poland

I had those samples but not a link to the study. They compared cranial from their samples(only ones they took DNA from? Didn't say) to Central European Neolithic and Mesolithic cranial. And said:

it was found that in terms of metric traits and cranial indices,the Brześć Kujawski group was closer to the Mesolithic populations of central Europe and the Eneolithic Funnel Beaker culture than to the Linear Pottery culture groups representing the first phase of Neolithization of this part of the continent.

Krefter
10-08-2015, 07:54 AM
I'm now putting my sites on East Asia, Central Asia, North Asia, and the Americas. I can already see there's lots of variation. It looks like there's more differentiation between differnt East Eurasians than between West Asians and Europeans. Also, there's a good amount of ancient mtDNA from China, Siberia, and Americas. A 40,000 year old mtDNA from China was East Asian-specific B and there's an around 8,000 year old B from China. There's mtDNA from Early Americans, Neolithic Siberians, Neolithic era Japan, and I think Bronze age China.Neolithic Siberian mtDNA is very differnt from modern East Siberian mtDNA I have. Maybe Siberians from the region those samples come from are more similar.

Also, I'll ask genome-bloggers if they are willing to do PCA, formal-stats, and ADMIXURE analysis of East Eurasians. I've already seen interesting trends.

Krefter
10-30-2015, 12:16 PM
I've finished working with over 1,000 samples from China, Korea, Mongolia, and Siberia. Soon I'll get data from Americas, Oceania, and Australia. I'm already getting familiar with the structure of East Asian mtDNA. There's a lot of diversity in Eastern mtDNA just as there is in Western mtDNA. Siberians don't look like they're basically Native American's brothers who stayed in Siberia. They have lots of mtDNA links to China/Korea that Native Americans don't.

It'll be interesting to see how South Asian-specific, Oceania, and Australian mtDNA relates to East Asian mtDNA. They have some-type of distant autosomal link and should share mtDNA lineages. For the most part I think the gene pools of Eastern Asia(including Oceania, Austrillia) and West Eurasia have been isolated for over 40,000 years. There could have be some common ancestry but certainly very little. Siberia/Central Asia(including Native Americans) and South Asia have received plenty of Western blood but besides that there's been complete isolation.

Krefter
01-15-2016, 12:56 PM
Australian Aboriginals and Papuans share very little mtDNA. Almost 100% of their mtDNA separated quickly after Non-African Founder lineages(N, M, R). There's essentially no sharing between East Asia/North Asia/America with Australians or Papuans. Autosomal DNA shows all non-Western Eurasians have significant shared ancestry, and Austrlians and Papuans have more after that, but I don't think it's very significant based on mtDNA.

Krefter
02-15-2016, 08:36 PM
Just collected 668 Mito-Genomes from Japan. The only non-East Asian haplogroup, appears to be R0*. So, a distant relative to R0s in West Eurasia(inclu. HV, H, R0a1a, etc).

Mellifluous
02-15-2016, 08:51 PM
Was W3a1 present in Anatolian Neolithic Farmers?

Krefter
02-15-2016, 08:53 PM
Was W3a1 present in Anatolian Neolithic Farmers?

No but one had W1c'i.

Krefter
02-18-2016, 10:00 PM
I finding new haplogroups like it's going out of style. Just added 2,000 new mito-genomes.

vettor
02-18-2016, 10:09 PM
Australian Aboriginals and Papuans share very little mtDNA. Almost 100% of their mtDNA separated quickly after Non-African Founder lineages(N, M, R). There's essentially no sharing between East Asia/North Asia/America with Australians or Papuans. Autosomal DNA shows all non-Western Eurasians have significant shared ancestry, and Austrlians and Papuans have more after that, but I don't think it's very significant based on mtDNA.

what about the mtdna of the Torres straits populace from NE-Australia ?

Krefter
02-18-2016, 10:41 PM
what about the mtdna of the Torres straits populace from NE-Australia ?

I have lots of mtDNA from that region.