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View Full Version : Awesome new study on the phylogeny of macrohaplogroup K Y-DNA



venustas
06-04-2014, 09:57 PM
Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia
http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2014106a.html
And I quote "Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a–d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R"
THE MP CLADE STILL EXISTS AND IT IS BEING RENAMED AS K2b
http://www.readcube.com/articles/10.1038/ejhg.2014.106?utm_campaign=readcube_access&utm_source=nature.com&utm_medium=purchase_option&utm_content=template2 snapshot of article.
http://snag.gy/FDjQU.jpg shows a highly informative table.
http://snag.gy/LqLuf.jpg is another great table.

venustas
06-04-2014, 10:04 PM
Does anyone have the paper here is the supplementary info.
http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg2014106s1.html?url=/ejhg/journal/vaop/ncurrent/abs/ejhg2014106a.html

If any of you control y-tree you need to update it.

Shaikorth
06-04-2014, 10:11 PM
Interestingly, the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania. Estimates of the interval times for the branching events between M9 and P295 point to an initial rapid diversification process of K-M526 that likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q.

So they go for East Eurasian "MNOPS" family.

RCO
06-04-2014, 10:17 PM
A major improvement in Greg Magoon's original insight
Generation of high-resolution a priori Y-chromosome phylogenies using “next-generation” sequencing data
http://dienekes.blogspot.com.br/2013/11/a-priori-y-chromosome-phylogeny-from.html

alan
06-04-2014, 10:21 PM
It shows that MPS split into south-east Asian MS on the one hand and north Eurasian P on the other.

venustas
06-04-2014, 10:22 PM
So they go for East Eurasian "MNOPS" family.

It includes the y-dna haplogroup R and Q. Which may be east Eurasian, and probably associated with some mtdna (R0-HV) that is also east Asian? In my opinion even if K did originate in east Asia it is western Eurasian because of it being in IJK, Eastern Eurasian can be defined as populations that have a high frequency of C y-dna and or M mtdna, and true east Asians do not exist anymore because they all have IJK-YDNA and (N)+R-MTDNA . I think east Asians are a hybrid between a Caucasian like people and a people that were more Eastern Asian then any group that exists today (This group was probably very dark). I think it would be cool if R- was East Asian in origin though. In any case I wonder what the paper says.

venustas
06-04-2014, 10:24 PM
Well seem than the new MP node idea has already been dismissed in this paper if I am understanding this right. It groups P, Q, R and K2b2. Anyone know anything about the latter.
No the MP clade still exists (relabled as K2b). However it includes S + K2 and K3 both found in oceania.

I wonder if the paper says where the K in the Philippine negritos fits on a tree.
K2 (P60) Mainly Australia and Melanesia.
K3 (P79) Mainly Australia and Melanesia
P (Q3, R1b,R1a, R2) Y-DNA
M Y-DNA
S Y-DNA

All of these belong to K2b previously known as MP.
However, 3 other subclades of K2 (also known as KXLT) exist one is surely NO+ X. I wonder what the other 2 are. Is all the K in Melanesia related to P?

alan
06-04-2014, 10:27 PM
The summary states 'the largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R'


No the MP clade still exists (relabled as K2b). However it includes S + K2 and K3 both found in oceania.

I wonder if the paper says were the K in the Philippine negritos fits on a tree.

RCO
06-04-2014, 10:34 PM
K2b=M+S+(K-P60)+(K-P79)+P(Q+R)
K2b1= M+S+(K-P60)+(K-P79)
K2b2= P(Q+R)

So the ancestors of Q and R definitely made a long trip from Southeast Asia to the American Continent and to Western Europe

venustas
06-04-2014, 10:35 PM
The summary states 'the largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R'

Yes but M is closer to P than it is to N or O.

alan
06-04-2014, 10:43 PM
So K2b is is like an M-P-S node. Still it is interesting that below that node there is a division that splits P from M and S. That is a pretty clear split between the far south-east and more northerly Eurasian groups. I must say though that I am a major skeptic of the idea that K originated in the far south-east and moved out from there because it appears to totally contradict archaeology. What I imagine is that the K2b1 branch that led to M and S made it east of India by a southern route early while the K2b2 branch perhaps remained constricted and west of India before passing by a northern route through central Asia. Otherwise we would need to envisage a retreat west towards SW Asia before a move north.


Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia
http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2014106a.html
And I quote "Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a–d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R"
THE MP CLADE STILL EXISTS AND IT IS BEING RENAMED AS K2b

alan
06-04-2014, 10:55 PM
I see what you mean. I was just saying that it makes M and S closer to each other than either are to P - not really surprising given the contrasting distribution.

I suppose if this was taken at face value - which I have doubts about - it would suggest a move from SW Asia after the IJK node which included a K element heading towards SE Asia with some then retreating back to SW Asia before heading north into central Asia and Siberia in P derived forms. It really doesnt fit the archaeological evidence though IMO, which points more to a route from Iran to the Stan central Asian countries to Siberia a little before 40000BC.

It always has to be borne in mind that it is possible that the positions of some of these apparently old populations was reached far later and the modern distribution may be misleading in some cases.


Yes but M is closer to P than it is to N or O.

RCO
06-04-2014, 11:13 PM
Nobody would leave the Indian Subcontinent to the Northern cold and arid mountains and plateaus, just the opposite. Probably the movement of K2b2 was following the littorals and just like haplogroup N from Indochina to China, Siberia. Follow the location of the biggest basal diversity to find the original source area.

parasar
06-05-2014, 01:30 PM
I see what you mean. I was just saying that it makes M and S closer to each other than either are to P - not really surprising given the contrasting distribution.

I suppose if this was taken at face value - which I have doubts about - it would suggest a move from SW Asia after the IJK node which included a K element heading towards SE Asia with some then retreating back to SW Asia before heading north into central Asia and Siberia in P derived forms. It really doesnt fit the archaeological evidence though IMO, which points more to a route from Iran to the Stan central Asian countries to Siberia a little before 40000BC.

It always has to be borne in mind that it is possible that the positions of some of these apparently old populations was reached far later and the modern distribution may be misleading in some cases.
The IJK node is also not necessarily west asian when we consider it in conjunction with South Asian H and SE Asian F.
Plus we should not forget the other K2s besides NO and MSP as phylogenetically they are all equally important.

Dubhthach
06-05-2014, 01:37 PM
Dienekes has the following image:

http://3.bp.blogspot.com/-W9tCYUPoeDo/U4_75fH8RPI/AAAAAAAAJnk/PeGLt4vWhk4/s1600/K-M526.png

From what I recall of the earlier study they didn't have a sample from a Haplogroup S man, so it's position wasn't known. Obvioulsy what's termed P331 in the above diagram is what was provisionally classed "MP", if they had a Haplogroup S sample back then they probably would have called it "MPS" (Aka. K2b)

-Paul
(DF41+)

alan
06-05-2014, 01:38 PM
It depends on the climate, hunting strategies and other factors. I agree heading north from India is unlikely for all sorts of reasons. Archaeology shows a movement from around Iran to Uzbekistan through central Asia to Altai, Baikal in the millenia around 40000BC eventually touching parts of NW China and Mongolia. For me that has simply got to be P and its derivatives R and Q. There is no evidence of a south to north movement further east than Iran. I dont know how M fits into this or K but IJK probably originated in SW Asia and IMO P took a northern route from around Iran. M and S seem to be unusual island groups restricted to the far SE and I wouldnt read a whole lot into such groups. It seems that the very common M-M4 is not that diverse according to Karafet and it could have arrived in New Guinea, Melanesia etc a huge time later than M came into existence.

I dont really like the idea of building the MP story on isolate populations but I would love to be able to read the paper. I dont know how old K is being dated so now since the SNP counting revolution. Anyone got an estimate? If there was some sort of retreat west it would be interesting to know the environment at the date of the split between M and P. There was of course the Phlegraean volcanic events the first of which was c. 40000 years ago and if that date still stands it makes it slightly later than the first modern humans in areas like Altai. That did have a bad effect on northern areas so perhaps that event drove some of MP south.


Nobody would leave the Indian Subcontinent to the Northern cold and arid mountains and plateaus, just the opposite. Probably the movement of K2b2 was following the littorals and just like haplogroup N from Indochina to China, Siberia. Follow the location of the biggest basal diversity to find the original source area.

parasar
06-05-2014, 02:22 PM
... P took a northern route from around Iran. M and S seem to be unusual island groups restricted to the far SE and I wouldnt read a whole lot into such groups. It seems that the very common M-M4 is not that diverse according to Karafet and it could have arrived in New Guinea, Melanesia etc a huge time later than M came into existence ...

For this to happen K2a, K2c, K2d, and K2e and many other still undetermined K-M526 all thousands of years apart made a beeline to SE Asia. Then from K2b, one P stayed around Iran, and MS made another beeline to remote Sahul. Does this even look plausible?

What looks to have happened is an earlier 50000ybp Austranesian* type expansion, except that that earlier expansion 50000ybp did not find any populated regions besides SubSaharanAfrica and spread rapidly all over.

*
http://upload.wikimedia.org/wikipedia/commons/0/0a/Migraciones_austronesias.png

RCO
06-05-2014, 02:34 PM
The correlation between geography and basal SNPs is quite clear in my opinion. M526 and P331 were Southeastern Asian SNPs from Indochina and the expansion of new SNPs below M526 were a result of the new Eastern expansions because we can find several branches adjacent to that regions towards to the South and East. Indochinha was full of peninsulas and islands http://en.wikipedia.org/wiki/Indochina creating new habitats and niches to new K2 branches. At that time Iran was the territory of IJ.

parasar
06-05-2014, 02:50 PM
The correlation between geography and basal SNPs is quite clear in my opinion. M526 and P331 were Southeastern Asian SNPs from Indochina and the expansion of new SNPs below M526 were a result of the new Eastern expansions because we can find several branches adjacent to that regions towards to the South and East. Indochinha was full of peninsulas and islands http://en.wikipedia.org/wiki/Indochina creating new habitats and niches to new K2 branches. At that time Iran was the territory of IJ.

Exactly, and it is also possible that there was no even in Iran 50000ybp.
Plus we should not discount the possibility, however unlikely it may seem, of an Oceanic expansion. Someone has to explain the potentially as old as 50000ybp Kimberley rock art.

"The Bradshaw Paintings are incredibly sophisticated, yet they are not recent creations but originate from an unknown past period which some suggest could have been 50,000 years ago." Peter Robinson, Project Controller of the Bradshaw Foundation.
In northern Australia, a mysterious form of rock art could legitimately be referred to as one of the seven wonders of the ancient world. Known as the Bradshaws, the art is dispersed in around 100 000 sites spread over 50 000 sq. km of northern Australia. Although the art's pigment can't be dated, a fossilised wasp nest covering one of the paintings has been dated at 17,000 + years old. This makes the art at least four times older than the pyramids of Egypt. It also makes the art a comparable age to the Grotte Chauvet paintings in France, which have been dated at 30,000-years-old. Although radio carbon dating was used to date the Grotte Chauvet pigments, the Bradshaw art can't be dated in the same way. Because they are so old, they have become part of the rock itself.

http://www.convictcreations.com/aborigines/images/bradshawboat1.jpg
http://www.convictcreations.com/aborigines/bradshaws.htm

Shaikorth
06-05-2014, 03:07 PM
The correlation between geography and basal SNPs is quite clear in my opinion. M526 and P331 were Southeastern Asian SNPs from Indochina and the expansion of new SNPs below M526 were a result of the new Eastern expansions because we can find several branches adjacent to that regions towards to the South and East. Indochinha was full of peninsulas and islands http://en.wikipedia.org/wiki/Indochina creating new habitats and niches to new K2 branches. At that time Iran was the territory of IJ.

C and D might have been further north at the time. And if we're talking of later periods (40,000 ya) what are the chances of Ust-Ishim turning out P?

parasar
06-05-2014, 03:30 PM
C and D might have been further north at the time. And if we're talking of later periods (40,000 ya) what are the chances of Ust-Ishim turning out P?

P is a pretty long string of SNPs, so somewhere along the line is possible.
The time to the most recent P(Q,R) though looks to be of lower age than Ust-Isim.

Edit:
On YFull I count 211 P equivalent and above SNPs till M1205.
YFull MP-M1205 level has 29 equivalent and above SNPs including Karafet et al's MSP-P331

venustas
06-05-2014, 05:16 PM
http://snag.gy/LqLuf.jpg
Shows that all of the K 1936 in New Guinea, is part of MPS or K2b, other than some O. It also makes it look like the Aeta have MPS (K2b) because MPS is present in South East Asia. However, I do not know what category K fits in Australia (other than one M found +modern R from Europe) , does any know what this table says 1937, or have access to the paper?

alan
06-05-2014, 05:34 PM
Doesnt seem implausible to me. Any pattern of fission is possible. I think we tend to think too much that branching follows a steady geographic wave of advance. I think its plausible that most of K2 tended to move east but P was an odd man out and headed north. However, in order to understand the context that could explain this in terms of environmental change etc we would really need agreed dates for the whole IJK and MNOP and MSP and MS and P nodes etc. Without agreed dates we cannot look at the context which might have led to the patterning. There were many important climatic changes, volcanos etc that might be important to understand the patterning.


For this to happen K2a, K2c, K2d, and K2e and many other still undetermined K-M526 all thousands of years apart made a beeline to SE Asia. Then from K2b, one P stayed around Iran, and MS made another beeline to remote Sahul. Does this even look plausible?

What looks to have happened is an earlier 50000ybp Austranesian* type expansion, except that that earlier expansion 50000ybp did not find any populated regions besides SubSaharanAfrica and spread rapidly all over.

*
http://upload.wikimedia.org/wikipedia/commons/0/0a/Migraciones_austronesias.png

Ebizur
06-05-2014, 05:35 PM
C and D might have been further north at the time. And if we're talking of later periods (40,000 ya) what are the chances of Ust-Ishim turning out P?

I think it is more likely that Ust-Ishim will turn out to be P* than any sort of C or D.

All human populations that inhabit the northern areas of Eurasia (as well as the indigenous populations of the Americas) belong predominantly to subclades of P, N, or (in some relatively limited areas) I or C2-M217 (the earliest known branch off the stem that has yielded the other extant subclades of C). The northern areas in which I or C2 are fairly common are also the ones that are most likely to have received some sort of influence from the south after their initial settlement by modern humans.

C(xC2) and D are essentially limited to southerly populations. I presume that K2 (and K2b in particular) has expanded so successfully by virtue of its being carried by the first modern human males to colonize some territories that were previously uninhabited by modern humans (lands disconnected from the Eurafrasian continent, northern wastelands of Eurasia, etc.).

alan
06-05-2014, 05:45 PM
My question is just how old is K? SNP dating seems to be pushing back dates by a fair bit. Are we now looking at a K node. I think I recall R being dated back to 30000 years and P to 40000 years. I imagine this would make K really very old.

alan
06-05-2014, 06:19 PM
I looked back and I think Michal calculated the age of K as 58.8 (50.1-77.3) years and P at around 40000 years old. That places around 20000 years between P and K based on the central dates. That is a very long period in which the MNOP then NO and MSP and finally MS and P nodes happened and plenty of time for all sorts of weird and wonderful things to happen. Another thing is the great age of K at c. 60000 years (and IJK just a little older) does pose archaeological questions. Of course there is nothing to say that K people moved just after the K node.

Ebizur
06-05-2014, 06:23 PM
My question is just how old is K? SNP dating seems to be pushing back dates by a fair bit. Are we now looking at a K node. I think I recall R being dated back to 30000 years and P to 40000 years. I imagine this would make K really very old.
According to Lippold et al. (2014), K is about 40,000 years old using "the fast mutation rate" and about 67,500 years old using "the slow mutation rate." The latter estimate is probably more accurate for the TMRCA of a haplogroup so old as K-M9.

parasar
06-05-2014, 06:50 PM
Doesnt seem implausible to me. Any pattern of fission is possible. I think we tend to think too much that branching follows a steady geographic wave of advance. I think its plausible that most of K2 tended to move east but P was an odd man out and headed north. However, in order to understand the context that could explain this in terms of environmental change etc we would really need agreed dates for the whole IJK and MNOP and MSP and MS and P nodes etc. Without agreed dates we cannot look at the context which might have led to the patterning. There were many important climatic changes, volcanos etc that might be important to understand the patterning.

Possible yes, but plausible? Say like, E stayed in Africa, while every other CT moved to Asia.
We tend to inflate phylogenetic value with current population levels, when in reality for K-M526 we have look at the situation 60000ybp. Y-P is just an insignificant twig in phylogenetic terms.

For P(Q,R), the dating IMO is quite secure based on both MA1 and Anzick1 - ~33000 years.
http://www.anthrogenica.com/showthread.php?1507-Some-provisional-calculations-for-haplogroup-R1a-based-on-the-first-FGC-result&p=41327&viewfull=1#post41327

For the separation of P from MS, we would have to go back perhaps another 20000 years.

alan
06-05-2014, 07:15 PM
I think I pretty well have given up on STR evidence for deep time dating and I would tend to believe the SNP counting estimate for K of c. 60000 years that Michal made above all the rest. His method checked out as correct with Mal'ta. That is not too far from the 2nd of those calculations anyway. One thing that I would immediately observe is that there is no evidence that is considered safe for human settlement in New Guinea etc until 47000 years ago at the earliest. So, on current evidence K and derivatives would have arrived a long long time after the K node itself. So, it appears it had a prior existence somewhere else c. 60000-45000BC.


According to Lippold et al. (2014), K is about 40,000 years old using "the fast mutation rate" and about 67,500 years old using "the slow mutation rate." The latter estimate is probably more accurate for the TMRCA of a haplogroup so old as K-M9.

parasar
06-05-2014, 07:16 PM
...
Shows that all of the K 1936 in New Guinea, is part of MPS or K2b, other than some O. It also makes it look like the Aeta have MPS (K2b) because MPS is present in South East Asia. However, I do not know what category K fits in Australia (other than one M found +modern R from Europe) , does any know what this table says 1937, or have access to the paper?

The line found in the aborigine hair was K-M526*.


From high-confidence Y-chromosome SNPs, we assigned his Y chromosome to the K-M526* macro-haplogroup (4). Although the O and P branches of haplogroup K-M526 account for the majority of East and West Eurasian Y chromosomes, the unresolved K-M526* lineages are more common (>5%) only among contemporary populations of Australasia (15, 18). Both uniparental markers fall within the known pattern found among contemporary Aboriginal Australians (15), providing further evidence that the genomic sequence obtained is not contaminated ...
The majority of paternal lineages in extant Aboriginal Australian and Melanesian populations
belong to region-specific sub-clades of haplogroups C and M, and to an unresolved paragroup
MNOPS (40, 44, 45)...

excluding it from assignment to haplogroups IJ, P and NO. Our filtering of the Y
chromosome sequence data with more relaxed settings allowed us to assign tentatively the hair
sample to para-clade MNOPS* by observing the C allele (with 10X depth) at rs2033003, M526
(Figure S22). The finding of ancestral alleles at M5 and M189 in the screen of unfiltered data
makes it unlikely that the sample would be further resolved within haplogroup M. While
considering Y chromosome haplogroup frequency data from modern-day populations, this
assignment is consistent with the donor of the sample having Aboriginal Australian, Melanesian
or Island Southeast Asian ancestry.


http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991479/

venustas
06-05-2014, 07:35 PM
The line found in the aborigine hair was K-M526*.


http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991479/

Yeah but that is a different study which had extremely poor Phylogenetic resolution. This study probably says its sampled some Australians who belonged to some type of K2b1.

The study ("Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asi) did sample aeta as evidenced by this screenshot http://snag.gy/UysKY.jpg

parasar
06-05-2014, 07:43 PM
I think I pretty well have given up on STR evidence for deep time dating and I would tend to believe the SNP counting estimate for K of c. 60000 years that Michal made above all the rest. His method checked out as correct with Mal'ta. That is not too far from the 2nd of those calculations anyway. One thing that I would immediately observe is that there is no evidence that is considered safe for human settlement in New Guinea etc until 47000 years ago at the earliest. So, on current evidence K and derivatives would have arrived a long long time after the K node itself. So, it appears it had a prior existence somewhere else c. 60000-45000BC.

K-M9 60000ybp and earlier was likely in upper SE Asia, Sunda portions now under water. Most unresolved M9 lines are in that region, Polynesia, Melanesia, and Australia. So not only K-M526 is diverse in the region but also K-M9.

We have a Vietnamese F-M89*, plus if I remember correctly even higher up a CT (xC, xM89), perhaps a B.

venustas
06-05-2014, 07:56 PM
K-M9 60000ybp and earlier was likely in upper SE Asia, Sunda portions now under water. Most unresolved M9 lines are in that region, Polynesia, Melanesia, and Australia. So not only K-M526 is diverse in the region but also K-M9.

Do you think any of the negritos belong to a brother of L or T?

parasar
06-05-2014, 07:59 PM
Yeah but that is a different study which had extremely poor Phylogenetic resolution. This study probably says its sampled some Australians who belonged to some type of K2b1.

The study did sample aeta as evidenced by this screenshot http://snag.gy/UysKY.jpg

Not able to clearly see the shot.
Is it this one?
http://mbe.oxfordjournals.org/content/27/8/1833/F2.medium.gif

venustas
06-05-2014, 08:07 PM
Not able to clearly see the shot.
Is it this one?
http://mbe.oxfordjournals.org/content/27/8/1833/F2.medium.gif
No thats the wrong article.
If you go to this link http://www.readcube.com/articles/10.1038/ejhg.2014.106 they allow you to see the first page of the article "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia" for free. However, the next four pages they blur up, so you only read the large text, however this blurred up text is searchable, and aeta popped up in text.

parasar
06-05-2014, 08:14 PM
Do you think any of the negritos belong to a brother of L or T?

There are L and T lines in S. Indian tribes. They are not negrito though as on mainland South Asia the negrito type is no longer prevalent except in isolation.

parasar
06-05-2014, 08:22 PM
No thats the wrong article.
If you go to this link http://www.readcube.com/articles/10.1038/ejhg.2014.106 they allow you to see the first page of the article "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia" for free. However, the next four pages they blur up, so you only read the large text, however this blurred up text is searchable, and aeta popped up in text.

Now I get it,:doh:
you are talking about the paper being discussed in this thread!
No I don't have it.

venustas
06-06-2014, 12:50 AM
you are talking about the paper being discussed in this thread!
No I don't have it.

After painstakingly researching Readcube for hours and guessing the letters in the search box I have discovered that


The article states that
"K-P378 is found exclusively among the aeta of the philippines and K"

venustas
06-06-2014, 12:51 AM
I find this fascinating. The Aeta of the Phillipines have been verfied to have K2b1 (Haplogroup MSK)

sahaliyan
06-06-2014, 10:36 AM
The P-P295* found in Aeta,Sulawesi,Sumba and Timor,sorry,guys,based on the evidence,P clearly has a Southeast Asian origin
1939

RCO
06-06-2014, 11:44 AM
Case closed: P has a Southeast Asian origin :P
How we would imagine that the major European Y haplogroup had had na origin in that "distant" part of the world ! The Euro masculinity were migrants or invaders derived from Indochina or Sundaland ! That's the beauty of Science and the beauty of genetic genealogy ! Well, how would my J1 Ancestors ever imagine that I could be here in South América as distant from the lands where hundreds of my Male generations and Y SNPs survived in the Northern Middle East and we could cross the big Oceans and move or invade a land in the Southern Hemisphere ! It happened to everybody !

parasar
06-06-2014, 12:41 PM
The P-P295* found in Aeta,Sulawesi,Sumba and Timor,sorry,guys,based on the evidence,P clearly has a Southeast Asian origin
1939

The phylogeny depicts a P1 besides P
Does the paper note the SNP for P1?
Also is there a P295+ P27- sample? If so in which population?
Thanks

Dubhthach
06-06-2014, 12:44 PM
28% P among the Aeta? Can't wait to tell my Filipina other half that I'm more "indigenous" than she is ;) *hides*

-Paul
(DF41+)

sahaliyan
06-06-2014, 12:55 PM
The phylogeny depicts a P1 besides P
Does the paper note the SNP for P1?
Also is there a P295+ P27- sample? If so in which population?
Thanks
The Aeta,Sulawesi,Sumba and Timor P-P205 samples are P295+ P27-

parasar
06-06-2014, 01:01 PM
The Aeta,Sulawesi,Sumba and Timor P-P205 samples are P295+ P27-

Wow!
So this splits the cluster of SNPs previously characterized as P or equivalent.


P 92R7_1, 92R7_2, F91/PF5862/V231, F1857/Page83/PF5901, L138, L268, L405/PF5990, L471/PF5989, L536/PF5860, L721/PF6020, L741/PF5960/YSC0000297, L768/PF5976/YSC0000274, L779/PF5907/YSC0000251, L781/PF5875/YSC0000255, M45/PF5962, M74/N12/PF5963, P27.1_1/P207, P27.1_2, P69, P226/PF5879, P228/PF5927, P230/PF5925, P235/PF5946, P237/PF5873, P239/PF5930, P240/PF5897, P243/PF5874, P244/PF5896, P281/PF5941, P282/PF5932, P283/PF5966, P284, P295/PF5866/S8...
http://www.isogg.org/tree/ISOGG_HapgrpP.html

soulblighter
06-06-2014, 01:04 PM
The P-P295* found in Aeta,Sulawesi,Sumba and Timor,sorry,guys,based on the evidence,P clearly has a Southeast Asian origin
1939

I think this has been a logical conclusion for atleast a few years now. This theory makes sense not only in a genetic sense, but paleoclimatology, geology and hydrology as well.

I wonder if Toba (70kybp) erupting and the prevailing winds taking all the toxic chemicals and ash clouds west from there towards the Indian subcontinent and NW from there (but not towards africa), decimated existing populations (D being a lone survivor) and so later maybe those east of Toba (yDNA K and mtDNA M) then migrated west and north, finding resources easily for rapid expansion without competition.

parasar
06-06-2014, 02:33 PM
I think this has been a logical conclusion for atleast a few years now. This theory makes sense not only in a genetic sense, but paleoclimatology, geology and hydrology as well.

I wonder if Toba (70kybp) erupting and the prevailing winds taking all the toxic chemicals and ash clouds west from there towards the Indian subcontinent and NW from there (but not towards africa), decimated existing populations (D being a lone survivor) and so later maybe those east of Toba (yDNA P and mtDNA M) then migrated west and north, finding resources easily for rapid expansion without competition.

These would be just the later stages from SE Asia say about 35000ybp. Obviously we have even later ones too Y-NO derivatives, and then in the historical period C3.

But post-Toba, I think an earlier prong went west from SE Asia, mainly Y-F derivatives, mtDNA N.

parasar
06-06-2014, 02:50 PM
mtDNA lineages in the Philippines today appear to have their origins
within the region of Southeast Asia and neighboring New Guinea (Tabbada et al.
2010; Gunnarsdottir et al. 2011). An extensive study of Y chromosomal DNA in
the Philippines showed that all negrito populations have a substantial component of
unresolved K*-M9 lineages, while a few have elements attributable to C*-RPS4Y,
both of which are presumed to predate the Austronesian expansion; the percentages
of these lineages was found to be particularly high among Aeta (87%, 100%) and
Agta (47%) populations of northern Luzon (Delfin et al. 2011). The distribution
of K*-M9 is not limited solely to groups defined as negrito, because it occurs at
a frequency of 67% among the Hanunuo of southern Luzon (Delfin et al. 2011).
... : 66% of Polynesian Y chromosomes are of Near Oceanian
origin, whereas 94% of Polynesian mtDNAs are of East Asian origin

http://digitalcommons.wayne.edu/cgi/viewcontent.cgi?article=2057&context=humbiol

parasar
06-06-2014, 04:21 PM
http://snag.gy/LqLuf.jpg

The above figure venustas had posted makes it quite clear where P295* originated and removes doubt that South Asia is a possibility (the South Asian P have to verified for P27). It is clear that it was from somewhere along Wallace's line (likely west), as it is absent in further west/north (continental Eurasia) and east/south (Oceania, Australia).

http://2.bp.blogspot.com/-qF-wb1LhiGY/Tmrm2RnLBCI/AAAAAAAAAoM/2f-E40KwGGo/s1600/Wallace-Line_3.jpg

soulblighter
06-06-2014, 05:06 PM
These would be just the later stages from SE Asia say about 35000ybp. Obviously we have even later ones too Y-NO derivatives, and then in the historical period C3.

But post-Toba, I think an earlier prong went west from SE Asia, mainly Y-F derivatives, mtDNA N.


Yes... I meant to type YDNA K. Not P.

I think P originated somewhere closer to NE India (Thailand/Myanmar?) rather than near the Wallace line though (but that is also a possibility I guess), on the way to becoming R and Q later further west.

parasar
06-06-2014, 06:17 PM
Yes... I meant to type YDNA K. Not P.

I think P originated somewhere closer to NE India (Thailand/Myanmar?) rather than near the Wallace line though (but that is also a possibility I guess), on the way to becoming R and Q later further west.

Wallace line is best possibility I think as it explains why P(Q, R) is to the west and north of it while closely related M and S are on its east and south. It also explains the lack of Denisovan in populations affected by P(Q, R). The location of M526 was quite clear since the 2008 Karafet paper, but P was a problem as we had no P from SE Asia (they were showing up as M526*). I had assumed Kostenki 14 was of S or SE Asian origin based on his (papuan-melanesian) physical characteristics, but we have no confirmation of his Y. Greg Magoon's paper gave us the first hints with shared MP SNPs, but now I think this current paper conclusively establishes the origination point with P* and P1.

I recall discussing Chianroni et al's centroids on DNA-Forums where I was of the opinion the centroids' "estimated" locations in almost uninhabited Tibet highlands for M526 (east) and P(west) were not likely and the centroids had to be pulled further SE to conform with "calculated" centroids for M and S.

parasar
06-06-2014, 10:50 PM
https://mcidublin.conference-services.net/reports/template/onetextabstract.xml?xsl=template/ onetextabstract.xsl&conferenceID=3958&abstractID=811773
C and D might have been further north at the time. And if we're talking of later periods (40,000 ya) what are the chances of Ust-Ishim turning out P?


O-15

The complete genome sequence of a 45,000-year-oldmodern human from Eurasia

Qiaomei Fu*1 ,2, Bence Viola1 ,3, Heng Li5 ,6, Priya Moorjani6, Flora Jay4, Aximu Ayinuer-Petri1, Susan Keates8, Yaroslav V. Kuzmin7, Montgomery Slatkin4, David Reich5 ,6, Janet Kelso1, Svante Pääbo1*
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,*2Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Beijing, China,*3Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,*4Department of Integrative Biology, University of California, Berkeley, USA,*5Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,6Department of Genetics,Harvard Medical School, Boston, USA,*7Institute of Geology & Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia,8University Village, Columbia, USA

*

We have sequenced to high coverage the genome of a femur recently discovered near Ust-Ishim in Siberia. The bone was directly carbon-dated to 45,000 years before present. Analyses of the relationship of the Ust-Ishim individual to present-day humans show that he is closely related to the ancestral population shared between present-day Europeans and present-day Asians. The over-all amount of genomic admixture from Neandertals is similar to that in present-day non-Africans and there is no evidence for admixture from Denisovans. However, the size of the genomic segments of Neandertal ancestry in the Ust-Ishim individual is substantially larger than in present-day individuals. From the size distribution of these segments we estimated that this individual lived about 200-400 generations after the admixture with Neandertals occurred. The age of this genome allows us to directly assess the mutation rate in the different compartments of the human genome. These results will be presented and discussed

parasar
06-07-2014, 04:45 PM
Yes... I meant to type YDNA K. Not P ...
There is not much of a daylight between the two.


The P331 mutation is derived in almost all K-M526 chromosomes ...

All P331 chromosomes tested are derived either at both P397 and P399 (haplogroup K2b1) or at P295 (haplogroup P or K2b2). ...

We consider a set of 68 mutations that were uniformly ascertained from resequencing studies ... Considering that we do not observe any of the 68 mutations occurring between the common ancestor of K-M9 chromosomes and that of K-P331 chromosomes, we estimate that this interval of time was shorter than 4.3% of the TMRCA of M168 chromosomes (95% upper bound). Assuming ~70 ky for the TMRCA of M168 chromosomes,10 we estimate the interval of time between the diversification of K-M9 and that of K-P331 to be <3 ky.



Amazing how just a couple of subset lines expanded so much while others stayed limited, perhaps isolated on islands.


the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania ...
Haplogroup P-P295 (K2b2) with sister clades Q and R is by far the most frequent haplogroup in Europe, the Americas, and Central and South Asia. ... Most of these newly described lineages are highly localized geographically to Island Southeast Asia/Oceania: K-P315 is confined to Melanesia ...

venustas
06-07-2014, 09:03 PM
http://en.wikipedia.org/wiki/Kusunda_language

Do any of you think the Kusanda language may be associated with haplogroup MPS (K2b) via the Indo pacific hypothesis?

Shaikorth
06-07-2014, 09:23 PM
https://mcidublin.conference-services.net/reports/template/onetextabstract.xml?xsl=template/ onetextabstract.xsl&conferenceID=3958&abstractID=811773


O-15

The complete genome sequence of a 45,000-year-oldmodern human from Eurasia

Qiaomei Fu*1 ,2, Bence Viola1 ,3, Heng Li5 ,6, Priya Moorjani6, Flora Jay4, Aximu Ayinuer-Petri1, Susan Keates8, Yaroslav V. Kuzmin7, Montgomery Slatkin4, David Reich5 ,6, Janet Kelso1, Svante Pääbo1*
1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,*2Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Beijing, China,*3Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany,*4Department of Integrative Biology, University of California, Berkeley, USA,*5Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,6Department of Genetics,Harvard Medical School, Boston, USA,*7Institute of Geology & Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia,8University Village, Columbia, USA

*

We have sequenced to high coverage the genome of a femur recently discovered near Ust-Ishim in Siberia. The bone was directly carbon-dated to 45,000 years before present. Analyses of the relationship of the Ust-Ishim individual to present-day humans show that he is closely related to the ancestral population shared between present-day Europeans and present-day Asians. The over-all amount of genomic admixture from Neandertals is similar to that in present-day non-Africans and there is no evidence for admixture from Denisovans. However, the size of the genomic segments of Neandertal ancestry in the Ust-Ishim individual is substantially larger than in present-day individuals. From the size distribution of these segments we estimated that this individual lived about 200-400 generations after the admixture with Neandertals occurred. The age of this genome allows us to directly assess the mutation rate in the different compartments of the human genome. These results will be presented and discussed

Looking at that, he's turning out to be autosomally like Tianyuan, equidistant to West Eurasians and East Eurasians.

venustas
06-08-2014, 05:15 AM
The orang asli are poorly studied .This study ,http://www.pnas.org/content/97/15/8225.full.pdf+html did a study on them and found out that at least 77% have O. 23 had either O or K if they did not belong to the right clade of O, or to something like N, or L or T or H, they were classied as K*. The orang asli mostly have O (77%) they do not have DE or D at all, and 23% of them have a type of K which could be archaic or not. In other words the Orang Asli are mostly just Asians and not negritos they have not relationship with the Andaman and no one knows if they have any magical K2b yet. Maybe they are ancestral to East Asians+ Artic Eurasians, while the people on the islands (Aeta, Melaesians) are ancestral to Indo-European and other Nostriaic peoples including native americans(R+Q)?

http://www.pnas.org/content/97/15/8225.full.pdf+html
phylogeny from here http://www.ncbi.nlm.nih.gov/pubmed/10577926
darn it orang asli is a catch all term "that includes 3 very distinct groups"
The batak are dominated by O y-dna http://www.academia.edu/3295810/Genetic_admixture_in_Batak_Negritos_in_Palawan

vettor
06-08-2014, 06:42 AM
Are many here, missing the point of K now?

By looking at the new breakup, does not K1 and k2a group still retain their plus 10000 years earlier "birth" than the K2b group?

How are some saying its a SE-Asia marker?

Clearly K1 and K2a did not venture beyond India/pakistan and most likely set up base on the BMAC/oxus areas )

next - where does it leave the split of the R marker then...........SE-Asia? or did it retain its R and split ob the road back to the subcontinent

parasar
06-08-2014, 03:46 PM
Looking at that, he's turning out to be autosomally like Tianyuan, equidistant to West Eurasians and East Eurasians.

Yes that was my first impression too, though we have to wait and see what kind of Asian is being referred to.

parasar
06-08-2014, 04:10 PM
Are many here, missing the point of K now?

By looking at the new breakup, does not K1 and k2a group still retain their plus 10000 years earlier "birth" than the K2b group?

How are some saying its a SE-Asia marker?

Clearly K1 and K2a did not venture beyond India/pakistan and most likely set up base on the BMAC/oxus areas )

next - where does it leave the split of the R marker then...........SE-Asia? or did it retain its R and split ob the road back to the subcontinent

Re: K1
The whole K-M9 group is likely of South East Asian origin. A study similar to this has to be done on the undifferentiated M9 lines in SE Asia and Oceania to see if they harbor LT-P326/L298.
There were some reports of T-M184 from Australia.

Re: K2a
No K2a has been found though there was a report of one pre- from S. India.
As far as N and O

It is suggested that it arose in southeast Asia 19.4±4.8 ky years ago, and then migrated in a counter-clockwise path from modern day regions of Mongolia and northern China to as far as northeastern Europe (Rootsi 2006).
http://en.wikipedia.org/wiki/Haplogroup_N_(Y-DNA)

Most researchers believe that O-M122 first appeared in Southeast Asia approximately 25,000-30,000 years ago (Shi 2009).
http://en.wikipedia.org/wiki/Haplogroup_O-M122_(Y-DNA)

Humanist
06-08-2014, 05:12 PM
There were some reports of T-M184 from Australia.

Can you provide links to the studies? I would be interested in reading further about T-M184 in Australia.

parasar
06-08-2014, 05:40 PM
Can you provide links to the studies? I would be interested in reading further about T-M184 in Australia.

I am trying to track source of that report down too.
The report was on the Wikipedia T page.

Family Tree DNA, a commercial genetic genealogy company, has displayed a map that shows a relatively high frequency of haplogroup T-M184 in some Australian aborigines. Probably the populations coincide with those previously reported in several studies as K*(M9), with a frequency near to 30% in Northern Australia. According to Family Tree DNA, the defining SNP for haplogroup T-M184 is M184, while M70 defines T1.[citation needed]

http://en.wikipedia.org/wiki/Haplogroup_T-M184
https://www.familytreedna.com/pdf-docs/2010-ydna-migration-map.pdf

venustas
06-08-2014, 05:45 PM
T is not in Australia this is speculation.K2B1 has been verified as the sole native type of K in Australia.

Humanist
06-08-2014, 05:46 PM
I am trying to track source of that report down too.
The report was on the Wikipedia T page.

http://en.wikipedia.org/wiki/Haplogroup_T-M184
https://www.familytreedna.com/pdf-docs/2010-ydna-migration-map.pdf

Thanks, Parasar. Though, hopefully we will get a better source than Wikipedia (referring to FTDNA). The Wikipedia page on T-M184 does not even list Assyrians and East Mizrahim Jews among the groups with the highest frequencies of Y-DNA T...


Highest frequencies: Somalis, Kurru, Bauris, Armenian Sasuntzis, Chians, Saccensi/Sicilians, Fulbe, Eivissencs, Northeastern Portuguese Jews, Rajus, Mahli, Zoroastrians in Kerman, Bakhtiaris/Lurs, Southern Egyptians.

parasar
06-08-2014, 05:49 PM
Thanks, Parasar. Though, hopefully we will get a better source than Wikipedia (referring to FTDNA). The Wikipedia page on T-M184 does not even list Assyrians and East Mizrahim Jews among the groups with the highest frequencies of Y-DNA T...
I agree, I was surprised too by that FTDNA map, it looks quite deliberate - as it has a two prong split in Australia.

parasar
06-08-2014, 06:24 PM
T is not in Australia this is speculation.K2B1 has been verified as the sole native type of K in Australia.

Have all regions of Australia been checked for P397/399 as K* is quite widespread?


Haplogroup K* or K(xLT,M,N,O,P,S) is by far the most common
haplogroup in South Australian Aboriginal groups (60%), a
situation reverse to that seen in most other samples of Aboriginal
males investigated to date. One report, however, found K* to
comprise 54% of 106 Y chromosomes from the N.T. [27]. Other
studies have reported frequencies of only 35% (Arnhem Land, [10]),
and 26% (Great Sandy Desert [10]). In the cases where less than ten
samples of Y chromosomes were typed [14,17,29] K* was absent,
but the Aboriginal male sample recently subject to genome-wide
analysis was K* [28]. Haplogroup K* is generally a very rare
haplogroup in world populations [13] but has among the highest
frequencies in Papua New Guinea (PNG) and Australian Aboriginal
populations [9]. Some PNG Ks have additional mutations that
define K sub lineages [29], but these have not been found in
Aboriginal Australians [9], with the exception of K2 (P308) [13].

http://www.agrf.org.au/assets/files/PDF%20Documents/Newsletter/FSIGEN%20Taylor%202012.pdf

"K* or more correctly K(xL,M,N,O,P,Q,R,S)"
"M168, M89 and M9 but the
ancestral allele for M130, M45 and M207 were typed for M20,
M186, LLY22g, M175 and M230 that define haplogroups L, M, N, O
and S, respectively."

vettor
06-08-2014, 06:39 PM
I agree, I was surprised too by that FTDNA map, it looks quite deliberate - as it has a two prong split in Australia.

The ftdna data looks flawed all the way , for T it has it at 10000 years , yet the paper states it ~15000 years older than R, which means T should be 40000 years old

The ftdna is a citation , its not proven and neither is this



The paternal haplogroup T-M70 varies between 3% and 24% of male lineages in Germany.

— The Genographic Project 2.0 2012


although this deals with M70 and not M184

vettor
06-08-2014, 06:45 PM
Have all regions of Australia been checked for P397/399 as K* is quite widespread?


http://www.agrf.org.au/assets/files/PDF%20Documents/Newsletter/FSIGEN%20Taylor%202012.pdf

"K* or more correctly K(xL,M,N,O,P,Q,R,S)"
"M168, M89 and M9 but the
ancestral allele for M130, M45 and M207 were typed for M20,
M186, LLY22g, M175 and M230 that define haplogroups L, M, N, O
and S, respectively."

This 2012 study shows zero for M184 in Australia

venustas
06-08-2014, 07:11 PM
. Modern Australians aborigines have K2b2(p) Mostly in the form of R1b1b2 because their brother decided to move back to the homeland :P of course. Unfortunately, their brothers brought among none K2b men who had E1b1b,I2, and maybe even T. Pure austalians aborigines are divided almost equally between two very very divergent groups C and K. Near All of their C belongs to a Australian specific subclade C-M347 which probably forms a clade with C-M38. Near all of their K is K2b1a1-P60 which is basically just a type of S y-dna. They do have M y-dna in the north (don't have time to get source yet) and they have Papuan blood in the north in some groups which is ancient. However, 1000+melanesians have been studied well and not 1 belongs to T, +25 Australian aborigines none belonged to T. If you want to wonder ask what y-dna do the semang in Malaysia have?

vettor
06-08-2014, 07:37 PM
. Modern Australians aborigines have K2b2(p) Mostly in the form of R1b1b2 because their brother decided to move back to the homeland :P of course. Unfortunately, their brothers brought among none K2b men who had E1b1b,I2, and maybe even T. Pure austalians aborigines are divided almost equally between two very very divergent groups C and K. Near All of their C belongs to a Australian specific subclade C-M347 which probably forms a clade with C-M38. Near all of their K is K2b1a1-P60 which is basically just a type of S y-dna. They do have M y-dna in the north (don't have time to get source yet) and they have Papuan blood in the north in some groups which is ancient. However, 1000+melanesians have been studied well and not 1 belongs to T, +25 Australian aborigines none belonged to T. If you want to wonder ask what y-dna do the semang in Malaysia have?

Not even the other original australians ( torres strait islanders ) have any T

this is the best I found for migration into australia

http://forwhattheywereweare.wordpress.com/2013/06/01/synthesis-of-the-early-colonization-of-asia-and-australasia-by-homo-sapiens-haploid-genetics/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885570/

parasar
06-08-2014, 07:40 PM
This 2012 study shows zero for M184 in Australia

They did not type M184 but used M20 as proxy to eliminate the LT group.
While I seriously doubt any T is present, upstream of LT may indeed be present, similar to say in SE Asia R, M207 not present, but upstream P295 is.

parasar
06-09-2014, 12:59 AM
Superb analysis by Maju at his blog: http://forwhattheywereweare.blogspot.co.nz/2014/06/y-dna-macro-haplogroup-k-m526.html
http://1.bp.blogspot.com/-xIyCVSPSm3I/U5LqVD5nawI/AAAAAAAACsM/TEjs1OTRu7k/s1600/Karafet-Y-DNA-K-tree-annotated.png

http://2.bp.blogspot.com/-jPSRG8AsE1Q/U5LtU89W2EI/AAAAAAAACsY/LsgDC0XZLas/s1600/Y-DNA-K-Sundaland.png

http://4.bp.blogspot.com/-wsNAS_dNkfg/U5L1ztBrjfI/AAAAAAAACso/DsrzZsJRtM4/s1600/Y-DNA-K-Sundaland-arrows.png


Overall this study underlies and vindicates my repeated claim of SE Asia playing also an important role in the formation of the Asian+ branch of Humankind, together with South Asia. Something I have repeatedly suggested is that mtDNA macro-haplogroup N appears to have coalesced in SE Asia, while its most prolific "daughter" R instead seems original from South Asia ... I am not sure on how exactly couple mtDNA N/R with the spread of Y-DNA K2 but it seems almost certain that they are related to a great extent.

lgmayka
06-09-2014, 01:11 AM
As far as N and O
http://en.wikipedia.org/wiki/Haplogroup_N_(Y-DNA)
Two men in the N-P189.2 clade have received Big Y results. Although the BAM files have not yet been evaluated by YFull, Chris Morley ran the VCF/BED files through his program. He found that, not counting SNPs at the level of N or above, and not counting "unresolved" SNPs:
- They share 153 SNPs distinctive to their clade, almost all not previously named
- They average 69 (64 vs. 74) private SNPs.

If we apply Michał's rule-of-thumb for VCF results (180 years per SNP), the two men in this exclusively European clade
- Diverged from the rest of N about 40,000 years ago
- Diverged from each other about 12,400 years ago.

parasar
06-09-2014, 01:47 AM
Two men in the N-P189.2 clade have received Big Y results. Although the BAM files have not yet been evaluated by YFull, Chris Morley ran the VCF/BED files through his program. He found that, not counting SNPs at the level of N or above, and not counting "unresolved" SNPs:
- They share 153 SNPs distinctive to their clade, almost all not previously named
- They average 69 (64 vs. 74) private SNPs.

If we apply Michał's rule-of-thumb for VCF results (180 years per SNP), the two men in this exclusively European clade
- Diverged from the rest of N about 40,000 years ago
- Diverged from each other about 12,400 years ago.

So this would mean that N-M231, NO(M214, P188, P192, P193, P194, P195), X (Magoon et al), and M526 are even older.

Something looks wrong with that 40000 age. If we go by Poznik et al, M231 is about half the age of M214, which is after that short interval (well <3kyrs) from K-M9 to K-M526.

http://stanfordcehg.files.wordpress.com/2014/02/f2-large.jpg

vettor
06-09-2014, 03:57 AM
Superb analysis by Maju at his blog: http://forwhattheywereweare.blogspot.co.nz/2014/06/y-dna-macro-haplogroup-k-m526.html
http://1.bp.blogspot.com/-xIyCVSPSm3I/U5LqVD5nawI/AAAAAAAACsM/TEjs1OTRu7k/s1600/Karafet-Y-DNA-K-tree-annotated.png

http://2.bp.blogspot.com/-jPSRG8AsE1Q/U5LtU89W2EI/AAAAAAAACsY/LsgDC0XZLas/s1600/Y-DNA-K-Sundaland.png

http://4.bp.blogspot.com/-wsNAS_dNkfg/U5L1ztBrjfI/AAAAAAAACso/DsrzZsJRtM4/s1600/Y-DNA-K-Sundaland-arrows.png

i like maju analysis from that site

It is implicit that neither L nor T have been found in SE Asia (no annotation in red) and that is also reflected in the arrows' map, where K2 (and not K as a whole) is shown arriving from South Asia.

What these chronological notes underline is that the expansion (split) of K, K2b and K2b1 (P) happened in "rapid" sequence with few millennia between each node.

Or in other words:
1. There was a split between K1 (LT) and K2 as this one migrated eastwards.
2. Then K2 split in Sundaland
2. Then K2b expanded in what is now Borneo.
3. Then P expanded from ~ Northern Borneo, with a branch (P1) back-migrating to South Asia.



where is sundaland?

Humanist
06-09-2014, 04:12 AM
i like maju analysis from that site

It is implicit that neither L nor T have been found in SE Asia (no annotation in red) and that is also reflected in the arrows' map, where K2 (and not K as a whole) is shown arriving from South Asia.

What these chronological notes underline is that the expansion (split) of K, K2b and K2b1 (P) happened in "rapid" sequence with few millennia between each node.

Or in other words:
1. There was a split between K1 (LT) and K2 as this one migrated eastwards.
2. Then K2 split in Sundaland
2. Then K2b expanded in what is now Borneo.
3. Then P expanded from ~ Northern Borneo, with a branch (P1) back-migrating to South Asia.


where is sundaland?

I posted the below bit on another forum a few years ago. I am curious whether there is a chance of any connection.

Morphometric analysis of the dentition from Bronze Age Tell Leilan, Syria, a contribution to the dental anthropology of ancient Mesopotamia (2001)


“Non-metric analysis of the permanent and deciduous dentition of the northern Mesopotamian Bronze Age site of Tell Leilan, when compared with similar analysis conducted world wide and in the Near East, reveals a relatively consistent affiliation with Western Eurasian, or Caucasoid populations, although certain traits share affinities to both Western Eurasian and Sunda-Pacific populations.”

Are any folks familiar with "Sunda-Pacific" populations? Is this, perhaps, what is meant?

Wikipedia:


Geologically, the Sunda Shelf is a south east extension of the continental shelf of Southeast Asia. Major landmasses on the shelf include the Malay Peninsula, Sumatra, Borneo, Java, Madura, Bali and their surrounding smaller islands.[1] It covers an area of approximately 1.85 million km2.[2] Sea depths over the shelf rarely exceed 50 metres and extensive areas are less than 20 metres resulting in strong bottom friction and strong tidal friction.[3] Steep undersea gradients separate the Sunda Shelf from the Philippines, Sulawesi and the Lesser Sunda Islands.

http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Map_of_Sunda_and_Sahul.png/661px-Map_of_Sunda_and_Sahul.png

parasar
06-09-2014, 04:19 AM
i like maju analysis from that site

It is implicit that neither L nor T have been found in SE Asia (no annotation in red) and that is also reflected in the arrows' map, where K2 (and not K as a whole) is shown arriving from South Asia.

What these chronological notes underline is that the expansion (split) of K, K2b and K2b1 (P) happened in "rapid" sequence with few millennia between each node.

Or in other words:
1. There was a split between K1 (LT) and K2 as this one migrated eastwards.
2. Then K2 split in Sundaland
2. Then K2b expanded in what is now Borneo.
3. Then P expanded from ~ Northern Borneo, with a branch (P1) back-migrating to South Asia.



where is sundaland?

Sundaland is supposedly the partly sunken SE Asian subcontinent, main remnants of which are the islands west of Wallace's line.
While I agree with most of Maju's analysis, if you look at Poznik's phylogeny and timeline, F-M89 to K-M526 is fast.
I doubt any long distance migration could have occurred in such a short period. Therefore I am of the opinion that F-M89 was itself a Sunda line.
Magoon et al

Tree “trunk” ... results for the 1000 Genomes Project sample HG02040 (Kinh population) indicate a
separation in SNPs defining the branch for haplogroup F (Hg-F). In particular, although HG02040 has most of the
key SNPs in common with other Hg-F samples, his results indicate ancestral results for three SNPs that are found to
be derived (or no-call) for all other Hg-F samples (including Hg-G, Hg-H, Hg-I, and Hg-J)


Of course if Toba resulted in not completely killing off Asians west of Toba, then there is chance some survivors moved to SE Asia in the way Maju suggests.

lgmayka
06-09-2014, 09:21 AM
If we go by Poznik et al, M231 is about half the age of M214, which is after that short interval (well <3kyrs) from K-M9 to K-M526.
Look again at the figure you posted. It refers to N-Page56. N-P189.2 tests negative for Page56, but positive for M231. FTDNA's new haplotree shows this correctly, apparently because they used one or more N-P189.2 examples from Geno 2.0. (In my own project, at least one N-P189.2 transferred Geno results; and the All Stories page of Genographic lists two Croatian N-M231 which are almost certainly N-P189.2.)

parasar
06-09-2014, 02:32 PM
Look again at the figure you posted. It refers to N-Page56. N-P189.2 tests negative for Page56, but positive for M231. FTDNA's new haplotree shows this correctly, apparently because they used one or more N-P189.2 examples from Geno 2.0. (In my own project, at least one N-P189.2 transferred Geno results; and the All Stories page of Genographic lists two Croatian N-M231 which are almost certainly N-P189.2.)

So you think M231 is much older than what appears in Poznik?
It will be interesting to see YFull's evaluation, especially comparisons with N1 - HG04015 ITU and K-M2335 - HG03742 ITU.

Shaikorth
06-09-2014, 03:06 PM
Ust-Ishim "clearly OOA, weakly in Asian clade". Looks like he was Tianyuan-ish as I suspected, and people that were either proto-Asian or pre-divergence were in Western Siberia 45k years ago.

parasar
06-09-2014, 03:51 PM
Ust-Ishim "clearly OOA, weakly in Asian clade". Looks like he was Tianyuan-ish as I suspected, and people that were either proto-Asian or pre-divergence were in Western Siberia 45k years ago.

Any information on mtDNA and/or Y? By Asian is it meant East Asian?


... with a branch (P1) back-migrating to South Asia.




This could work if K-M9 is ~55000 years old which would give us P1 as 35000 (55-(3+5+12)) years and sufficient time to get to the Baikal in pre-R derivative form by 24000ybp.

Shaikorth
06-09-2014, 03:59 PM
Any information on mtDNA and/or Y? By Asian is it meant East Asian?




I was forced to rely on tweets, but it seems haplogroups were not mentioned. Autosomally he was "clearly OOA, weakly in Asian clade but close to anc of Eurasia", and the best way to interpret that IMO is that he's in the East Eurasian clade as opposed to West Eurasian clade, but close to root.

lgmayka
06-09-2014, 06:23 PM
So you think M231 is much older than what appears in Poznik?
Yes, because Poznik is really referring to Page56. M231 is much older.

Part of the confusion comes from LLY22g. Academics have found many examples of M231+ LLY22g- , and they mistakenly believe that such examples are the "earliest" N. But we now have multiple examples showing that LLY22g is rather unstable, and cannot be reliably used as a SNP for 40,000-year-old haplogroups.

vettor
06-09-2014, 06:33 PM
Yes, because Poznik is really referring to Page56. M231 is much older.

Part of the confusion comes from LLY22g. Academics have found many examples of M231+ LLY22g- , and they mistakenly believe that such examples are the "earliest" N. But we now have multiple examples showing that LLY22g is rather unstable, and cannot be reliably used as a SNP for 40,000-year-old haplogroups.

there is a dozen people in modern croatia/bosnia belonging to Haplogroup N (LLY22G)Uralic-speaking peoples who "migrated" from the southern Siberia region into western Europe around 8,000BC. Clearly this marker is older than 10000 years old

lgmayka
06-09-2014, 08:26 PM
there is a dozen people in modern croatia/bosnia belonging to Haplogroup N (LLY22G)Uralic-speaking peoples who "migrated" from the southern Siberia region into western Europe around 8,000BC. Clearly this marker is older than 10000 years old
You can find some South Slavic N-P189.2 in YHRD by searching for

DYS393 = 14
DYS390 = 25
DYS19 = 14
DYS391 = 10
DYS385 = 11-16
DYS392 = 14

This search finds

n of N Geoposition [Population]
2 of 215 Novi Sad, Serbia [Serbian]
2 of 220 West Croatia, Croatia [Croatian]
1 of 257 Ljubljana, Slovenia [Slovenian]
1 of 220 East Croatia, Croatia [Croatian]
1 of 629 Eastern Slovakia, Slovakia [Slovakian]
1 of 31 Doboj-Banja Luka-Bjeljina, Bosnia and Herzegowina [Bosnian]

But this is only one cluster. I have found unclustered members of N-P189.2 in the Netherlands, Italy, and France.

parasar
06-10-2014, 02:31 AM
I was forced to rely on tweets, but it seems haplogroups were not mentioned. Autosomally he was "clearly OOA, weakly in Asian clade but close to anc of Eurasia", and the best way to interpret that IMO is that he's in the East Eurasian clade as opposed to West Eurasian clade, but close to root.

Looks like some kind of a YAP is a possibility, I'm having trouble with coming up with anything else that would work for both "clearly OOA" [which I construe as back to Africa in this time-frame] and "weakly in Asian clade."

venustas
06-10-2014, 03:02 AM
Looks like some kind of a YAP is a possibility, I'm having trouble with coming up with anything else that would work for both "clearly OOA" [which I construe as back to Africa in this time-frame] and "weakly in Asian clade."
Do you have direct evidence for that? I hope so? He had mtdna hg R and that is verified. http://snag.gy/IzthP.jpg

parasar
06-10-2014, 03:17 AM
Do you have direct evidence for that? I hope so? He had mtdna hg R and that is verified. http://snag.gy/IzthP.jpg

No. I had seen that tweet, and mtDNA R would point to the east Asian side, but I'm not able to figure out how the autosomal evidence is showing clearly OOA, that was the reason for the YAP guess.
https://pbs.twimg.com/media/Bpsmqs8CYAARPV3.jpg

venustas
06-10-2014, 03:21 AM
No. I had seen that tweet, and mtDNA R would point to the east Asian side, but I'm not able to figure out how the autosomal evidence is showing clearly OOA, that was the reason for the YAP guess.
https://pbs.twimg.com/media/Bpsmqs8CYAARPV3.jpg MTDNA R does not point to the east Asian side mtdna M does, but R this old, suggests this guy is connected to Caucasians distantly. Europe=90% R , east asia =35% R. Because he had R MTDNA I think he had some type of F y-dna, whether it be G,H,NO*, or P. Of course he was related to Asians, somewhat at least.

parasar
06-10-2014, 03:39 AM
MTDNA R does not point to the east Asian side mtdna M does, but R this old, suggests this guy is connected to Caucasians distantly. Europe=90% R , east asia =35% R. Because he had R MTDNA I think he had some type of F y-dna, whether it be G,H,NO*, or P. Of course he was related to Asians, somewhat at least.

Not to me, much of diversity of R lies in East Asia. Staring with U, R0 we see a movement towards west Eurasia.
Maju who I had quoted above is of the opinion that:

Overall this study underlies and vindicates my repeated claim of SE Asia playing also an important role in the formation of the Asian+ branch of Humankind, together with South Asia. Something I have repeatedly suggested is that mtDNA macro-haplogroup N appears to have coalesced in SE Asia, while its most prolific "daughter" R instead seems original from South Asia ... I am not sure on how exactly couple mtDNA N/R with the spread of Y-DNA K2 but it seems almost certain that they are related to a great extent.

To me even R should be considered East Eurasian and not South Asian (ie on the West Eurasian side).

venustas
06-10-2014, 04:00 AM
Not to me, much of diversity of R lies in East Asia. Staring with U, R0 we see a movement towards west Eurasia.
Maju who I had quoted above is of the opinion that:

To me even R should be considered East Eurasian and not South Asian (ie on the West Eurasian side).
I think some R may have originated in East Asia, but it is essentially western Eurasian. Its just a lot of the Western Eurasians descend from a melanesioid people who lived in East Asia. The diversity of K2b y-dna and N mtdna in asia is mostly the fault of australoids.
http://biorxiv.org/content/biorxiv/suppl/2014/01/13/001792.DC1/001792-1.pdf Shows a bootstrap phylogenic tree for mtdna http://snag.gy/l5907.jpg. According to this the haplogroup R0 mtdna closest relatives are P and B mtdna. It may be possible that a population from Indonesia, with K2b2 and pre-R0 mtdna are responsible for a large genetic component of western Eurasia.

parasar
06-10-2014, 04:17 AM
I think some R may have originated in East Asia, but it is essentially western Eurasian. Its just a lot of the Western Eurasians descend from a melanesioid people who lived in East Asia. The diversity of K2b y-dna and N mtdna in asia is mostly the fault of australoids.

This I could agree with, with the qualifier "now essentially western Eurasian," and that is why sometimes it difficult to call these east or west when we are talking 45000ybp or beyond. Modern humans were living in East Asia at least 100000ybp.


Later Paleolithic Man of China — Liujiang and Upper-Cave Man — can also clearly distinguished from the rest of Neolithic Man in China in the scattergram, and can be considered as two different local types of Later Paleolithic Man. So-called “Negro-Australoid” racial traits can themselves be doubtlessly traced back to Later Paleolithic Man of China — Liujiang and Upper-cave Man

http://link.springer.com/article/10.1007%2FBF02436421


The age and morphology of the Zhiren Cave human remains support a modern human emergence scenario for East Asia involving dispersal with assimilation or populational continuity with gene flow. It also places the Late Pleistocene Asian emergence of modern humans in a pre-Upper Paleolithic context and raises issues concerning the long-term Late Pleistocene coexistence of late archaic and early modern humans across Eurasia

http://www.pnas.org/content/early/2010/10/15/1014386107.abstract


In the former case, which is better supported, the fossils would date to at least ∼68 ka, but more likely to ∼111–139 ka. Alternatively, they would be older than ∼153 ka. Both scenarios would make the Liujiang hominid one of the earliest modern humans in East Asia

http://www.sciencedirect.com/science/article/pii/S0047248402906019


The 2007 discovery of fragmentary human remains (two molars and an anterior mandible) at Zhirendong (Zhiren Cave) in South China provides insight in the processes involved in the establishment of modern humans in eastern Eurasia. The human remains are securely dated by U-series on overlying flowstones and a rich associated faunal sample to the initial Late Pleistocene, >100 kya. As such, they are the oldest modern human fossils in East Asia and predate by >60,000 y the oldest previously known modern human remains in the region.

http://www.pnas.org/content/107/45/19201.full

vettor
06-10-2014, 07:12 AM
This could work if K-M9 is ~55000 years old which would give us P1 as 35000 (55-(3+5+12)) years and sufficient time to get to the Baikal in pre-R derivative form by 24000ybp.

http://dispatchesfromturtleisland.blogspot.com.au/2014/06/most-northern-hemisphere-men-have.html

above some some years of age

as for T and L , well they are early Neolithic and/or Epipaleolithic

Epipaleolithic = between the end of hunter gatherers period and the start of early farmers period

vettor
06-10-2014, 07:19 AM
This I could agree with, with the qualifier "now essentially western Eurasian," and that is why sometimes it difficult to call these east or west when we are talking 45000ybp or beyond. Modern humans were living in East Asia at least 100000ybp.


http://link.springer.com/article/10.1007%2FBF02436421


http://www.pnas.org/content/early/2010/10/15/1014386107.abstract


http://www.sciencedirect.com/science/article/pii/S0047248402906019


http://www.pnas.org/content/107/45/19201.full

Let us bring some logic into it
If the old system states:
from F
came GHIJKLT
then G split fromHIJKLT
then H split from IJKLT
then IJ split form KLT
then I split and J split and LT split from K

does this not mean that these haplogroups split before P was even formed from K ?

does this not indicate M, P, X and S arrived before R?

does this not indicate that since MPX and S are in south-east asia and R was not formed that R for all logic must be also in south-east asia?

parasar
06-10-2014, 02:31 PM
Let us bring some logic into it
If the old system states:
from F
came GHIJKLT
then G split fromHIJKLT
then H split from IJKLT
then IJ split form KLT
then I split and J split and LT split from K

does this not mean that these haplogroups split before P was even formed from K ?

does this not indicate M, P, X and S arrived before R?

does this not indicate that since MPX and S are in south-east asia and R was not formed that R for all logic must be also in south-east asia?

vettor,

The exchange above was in reference to Ust-Ishim's mtDNA R. As far as Y-R is concerned, I think that it is much later and need not have originated in SE Asia and most likely did not, only its precursors did.

parasar
06-12-2014, 03:30 AM
Thanks, Parasar. Though, hopefully we will get a better source than Wikipedia (referring to FTDNA). The Wikipedia page on T-M184 does not even list Assyrians and East Mizrahim Jews among the groups with the highest frequencies of Y-DNA T...

Is there any particular STR signature to look for in M184?
Maldives is almost as south as you can get in South Asia and it seems to have a lot of K(xL,M,NO,P,S,T). http://onlinelibrary.wiley.com/store/10.1002/ajpa.22256/asset/supinfo/ajpa22256-sup-0010-suppinfo6.xlsx?v=1&931292c1
As only M70 was typed (http://onlinelibrary.wiley.com/store/10.1002/ajpa.22256/asset/supinfo/ajpa22256-sup-0006-suppinfo2.doc?v=1&02f1bd7a), I was wondering if these K(xL,M,NO,P,S,T) could be M184.


10 major haplogroups: A(M191), C(M130), F*(xG,H,I,J,K), G(M201), H(M69), J(M304), K*((xL,M,NO,P,S,T), L(M20), Q(M242), and R(M207) (Fig. 3; detailed results per island sample are in Supporting Information Figs.S2 and S3). The most prevalent haplogroups are F*(xG,H,I,J,K), H(M69), J(M304), L(M20), and R(M207), that combined correspond to 90% of the individuals. Globally, the highest frequencies of haplogroups F*(xG,H,I,J,K), H(M69) (including H(M69)(xH1(M52)) and H1(M52)) and L(M20) are found in the Central reference population, that is, South Asia, whereas they are rare outside this region. The haplogroup J(M304) Y chromosomes are all in subgroup J2(M172). This haplogroup is found at high frequencies in Southwest Asia, in our Western reference population, and in the Caucasus; in South Asia it is widespread at frequencies below 10%, mainly in caste populations. The haplogroup R(M207) Y chromosomes are in subgroups, R1a1a(M17) and R2a(M124) ... the [B]K*(xL,M,NO,P,S,T (4%) ... individuals appear to form a monophyletic cluster ...

http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22256/full

vettor
06-12-2014, 05:59 AM
Is there any particular STR signature to look for in M184?
Maldives is almost as south as you can get in South Asia and it seems to have a lot of K(xL,M,NO,P,S,T). http://onlinelibrary.wiley.com/store/10.1002/ajpa.22256/asset/supinfo/ajpa22256-sup-0010-suppinfo6.xlsx?v=1&931292c1
As only M70 was typed (http://onlinelibrary.wiley.com/store/10.1002/ajpa.22256/asset/supinfo/ajpa22256-sup-0006-suppinfo2.doc?v=1&02f1bd7a), I was wondering if these K(xL,M,NO,P,S,T) could be M184.

M184 is a basal marker of T you do not need to have it . You could have M272 instead ( I have M184 in 23andme and do not have it in natgeno2 nor in ftdna .........you tell me whats going on , I have M272 in all 3 )

M70 makes a T person into a T1 person , again there are T people without M70...........germany and syria come to mind

Humanist
06-12-2014, 06:23 AM
M70 makes a T person into a T1 person , again there are T people without M70...........germany and syria come to mind

There is an Assyrian (from Iraq, Iran, or Turkey) in an unpublished dataset that is categorized as K-M9* (xM70...). The man was not tested for T-M184.

vettor
06-12-2014, 06:40 AM
There is an Assyrian (from Iraq, Iran, or Turkey) in an unpublished dataset that is categorized as K-M9 (xM70). The man was not tested for T-M184.

I do not understand...is he another T basal marker........below are the basal ones only

L445,
L452,
L455/PF5670,
CTS7749/L810/PF5640,
M184/Page34/USP9Y+3178,
M272/PF5667,
Page129

Humanist
06-12-2014, 06:43 AM
I do not understand...is he another T basal marker........below are the basal ones only

L445,
L452,
L455/PF5670,
CTS7749/L810/PF5640,
M184/Page34/USP9Y+3178,
M272/PF5667,
Page129

He is either a basal T or a genuine M9*. I would bet on the former.

parasar
06-13-2014, 09:59 PM
I posted the below bit on another forum a few years ago. I am curious whether there is a chance of any connection.

Morphometric analysis of the dentition from Bronze Age Tell Leilan, Syria, a contribution to the dental anthropology of ancient Mesopotamia (2001)



Are any folks familiar with "Sunda-Pacific" populations? Is this, perhaps, what is meant?

Wikipedia:



http://upload.wikimedia.org/wikipedia/commons/thumb/5/5f/Map_of_Sunda_and_Sahul.png/661px-Map_of_Sunda_and_Sahul.png

Bronze Age would be a little too late for direct input from Sundaland, though indirectly though the Indus Valley is quite possible.
The neolithic population of Mehrgarh had Sundadont type dentition.

Please see also:
Hanihara T.1992c.Negritos, Australian aborigines, and the "proto-sundadont" dental pattern: the
basic populations in East Asia, V. American Journal of Physical Anthropology, 88(2):183-196.

venustas
06-16-2014, 06:49 PM
Assuming
B70 ky for the TMRCA of M168 chromosomes,10 we estimate the
interval of time between the diversification of K-M9 and that of
K-P331 to be o3 ky. This rapid diversification has also been assessed
using whole Y-chromosome sequence data.22 In addition, we estimate
the total time between the common ancestor of K-M9 and that of
P-P295 to be o5 ky, and the time between the common ancestor
P-P295 and that of P-P27 to be 12.3 ky (95% CI: 6.6–20 ky).
-----------------------------------------------------------------
Incidentally, the Y chromosome obtained from an
B100-year-old lock of hair in Australia, initially identified as
K-M526*,20 carries the derived allele at P304.
------------------------------------------------------------------------------------
The P295 mutation,
previously assumed to be equivalent to 18 other mutations defining
the haplogroup P,10 is derived in a broader group of chromosomes.
In our worldwide sample of 7462 Y chromosomes, we observe the
newly defined paragroup P-P295* in 83 chromosomes from Island
Southeast Asia (Timor, Sumba, Sulawesi) and the Negrito Aeta
population from Philippines (Table 1 and Figure 2).
-----------------------------------------

Chad Rohlfsen
06-16-2014, 09:17 PM
Ust-Ishim is pre-East/West split. It would make no sense to have an East Eurasian 2000mi west of Mal'ta, 21k years prior, and leave no genetic trace in North Eurasia. Mal'ta is the oldest diverged person, to this point. Mal'ta and La Brana have no East Eurasian aDNA. There was no such thing as East Eurasian going back into the root of k2. North Eurasians did not contribute a great deal to West Eurasian ancestry outside of Southern Asia, like Afghanistan. There's nothing over 20% in Europe.

parasar
06-17-2014, 07:05 PM
Ust-Ishim is pre-East/West split. It would make no sense to have an East Eurasian 2000mi west of Mal'ta, 21k years prior, and leave no genetic trace in North Eurasia. Mal'ta is the oldest diverged person, to this point. Mal'ta and La Brana have no East Eurasian aDNA. There was no such thing as East Eurasian going back into the root of k2. North Eurasians did not contribute a great deal to West Eurasian ancestry outside of Southern Asia, like Afghanistan. There's nothing over 20% in Europe.
That would depend on how you define East Eurasian, genetically or geographically. Genetically in an early period the populations in East Eurasia were more Australoid-Negroid like and not like current East Eurasians. It is only later that the population that we now think of as East Eurasian arose, which must have happened post occupation of America as early Americans were also of the Australoid-Negroid type.


Later Paleolithic Man of China — Liujiang and Upper-Cave Man — can also clearly distinguished from the rest of Neolithic Man in China in the scattergram, and can be considered as two different local types of Later Paleolithic Man. So-called “Negro-Australoid” racial traits can themselves be doubtlessly traced back to Later Paleolithic Man of China — Liujiang and Upper-cave Man. These traits are the intrinsic characteristics of Neolithic Man in China and only then is there slight difference in the extent of the manifestation of these traits in the population.
http://link.springer.com/article/10.1007%2FBF02436421


A formal taxonomic review defines the early Paleoindian groups as Otomid-Sundadonts...

http://www.ncbi.nlm.nih.gov/pubmed/16176057

Shaikorth
06-17-2014, 07:35 PM
That would depend on how you define East Eurasian, genetically or geographically. Genetically in an early period the populations in East Eurasia were more Australoid-Negroid like and not like current East Eurasians. It is only later that the population that we now think of as East Eurasian arose, which must have happened post occupation of America as early Americans were also of the Australoid-Negroid type.

http://link.springer.com/article/10.1007%2FBF02436421


http://www.ncbi.nlm.nih.gov/pubmed/16176057

The so-called Paleoamericans seem to be like modern Native Americans mtdna-wise, and autosomally in all likelihood as well. Anzick-1 is interchangeable with Karitiana - an ANE/"East Asian" mix - and I'll be very surprised if anything earlier and more southern than him will turn out not like that. If physical anthropology is at odds with genetics, I'm inclined to dismiss the former.

I have linked this (http://www.diva-portal.org/smash/get/diva2:667495/FULLTEXT01.pdf) (pages 39-41) before, but it's a good warning about relying on physical metrics when measuring old skeletal remains - 300 year old bones from Swedish individuals who according to physical anthropology were Native Americans and Chinese (not even intermediate Eurasians), were genetically identical to the ones classified as europeans. What does that say about reliability of physical metrics when it comes to 15,000 years old remains?

Archaic East Asians in general do not show increased affinity to Australoids compared to modern East Asians. Tianyuan seems to be slightly more related to East Asians and Europeans than to Papuans and Melanesians, and supposedly Ust-Ishim, earlier and much more western geographically, is slightly more related to East Asians than to other Eurasian populations.

parasar
06-17-2014, 07:49 PM
The so-called Paleoamericans seem to be like modern Native Americans mtdna-wise, and autosomally in all likelihood as well. Anzick-1 is interchangeable with Karitiana - an ANE/"East Asian" mix - and I'll be very surprised if anything earlier and more southern than him will turn out not like that. If physical anthropology is at odds with genetics, I'm inclined to dismiss the former.
...

Does Anzick-1 have the EDAR mutation (because straightening of hair and sino-dentition would require that)? If not, when did that come in, as it now reaches fixation levels in East Asia and the Americas. If it did, is it possible that what we term as East Asian characteristics are actually of American origin?

parasar
06-17-2014, 07:56 PM
...
Archaic East Asians in general do not show increased affinity to Australoids compared to modern East Asians. Tianyuan seems to be slightly more related to East Asians and Europeans than to Papuans and Melanesians, and supposedly Ust-Ishim, earlier and much more western geographically, is slightly more related to East Asians than to other Eurasian populations.

Tianyuan is actually closest to the geographically distant Karitiana than to the current Han living in Tianyuan's neighborhood. The higher Denisovan remnants in modern Papuans and Australians makes them distant too.

Shaikorth
06-17-2014, 08:02 PM
Does Anzick-1 have the EDAR mutation (because straightening of hair and sino-dentition would require that)? If not, when did that come in, as it now reaches fixation levels in East Asia and the Americas. If it did, is it possible that what we term as East Asia characteristics are actually of American origin?

I haven't managed to find anything about Anzick-1 and EDAR. It's likely that it wasn't sequenced, because derived or ancestral status for it would surely have been mentioned like it was for MA-1.

EDAR's place of origin is hard to say. Assuming Native American origin, Siberians should have higher levels than East Asians, and East Asia should have a cline with Japanese and North Han Chinese having more frequently the derived variant than She and South Han.
http://oi58.tinypic.com/x2mr5x.jpg
It's quite clear that North Han and Japanese have a Native American shift compared to She and South Han, but this is likely just some ANE admixture as they also have higher South Asian shift despite greater geographic separation.

Edit.
Tianyuan is also more shifted towards She and Orcadians than Karitiana. Since She are among the purest examples of "East Asian" it's hard to say anything about Tianyuan except that it's pre-divergence.

parasar
06-17-2014, 08:46 PM
I haven't managed to find anything about Anzick-1 and EDAR. It's likely that it wasn't sequenced, because derived or ancestral status for it would surely have been mentioned like it was for MA-1.

EDAR's place of origin is hard to say ...

That is what I looking for, as that mutation correlates well with sino-dentition (if it is not causal), and as I had mentioned early Americans were Otomid-Sundadonts. So I would expect them to be EDAR negative much like MA-1. This variation is dentition is not known to provide any specific advantage.

EDAR variant:
http://ars.els-cdn.com/content/image/1-s2.0-S0092867413000676-gr1.jpg
http://www.cell.com/cell/abstract/S0092-8674(13)00067-6

If the very earliest Americans did not have EDAR, and if it did not arise among them and go to East Asia, then there are two possibilities - EDAR arose independently or the there was a later influx. We have to wait and see how this plays out.

Sein
06-17-2014, 08:56 PM
I just wanted to make note of an exceedingly minor personal detail concerning EDAR. Most analyses show that I have 4% Siberian/Northeast Asian admixture, which one wouldn't expect to leave much of a phenotypic impact. My mother has 0% Siberian/Northeast Asian admixture, so I think my father is probably around 8%. Even 8% doesn't feel like a substantial amount if we are dealing with effects on physical appearance. Yet, both myself and my father resemble Uzbeks/Tajiks, and we could also easily blend in among more Central Asian-looking Chechen people, as well as other groups in the Caucasus who show hints of East Asian admixture in their facial features. Here in the US, I'm always confused for a Hispanic (albeit an extraordinarily hirsute and beaky nosed one). You could probably arrive at my phenotype by mixing 75% Iranian with 25% Mongolian. Before I got into autosomal testing, it was my working assumption that I'd turn out to be at least 15% Siberian ENA. A meager 4% was quite a shock. So, I think it really boils down to EDAR. I'm a heterozygote for that SNP, and I have coarse/thick/extremely straight hair, tooth shoveling, and a slight development of epicanthic folds over my eyes. My mother has the ancestral alleles at this SNP, so my father definitely has the East Asian form of the mutation.

To make a long story short, I think many of the features which distinguish modern East Asians from West Eurasians (Europeans, Near Easterners, and South Asians) are a byproduct of this single mutation. The only East Asian-specific features which I think don't go with this mutation are glabrousness, facial flatness, and a lack of nasal projection. Both myself and my father are extremely hirsute (if you are more hirsute than us, you don't really qualify for the Homo sapiens sapiens label, as I think we are at the limit of normality for this trait among males, :biggrin1:), our faces are prominent, and our noses are basically the kind that are usually associated with the people of the Iranian plateau. Many Native Americans with 0% European admixture have very projective noses/projective faces, and they are almost fixed for EDAR, so that part of the East Asian phenotypic complex must have another genetic foundation. I'm not sure if the development of epicanthic folds have been correlated with EDAR, but I think there could be a connection.

parasar
06-17-2014, 10:01 PM
I had explained my logic before on current closeness vs ancestral closeness using the Y locus (and this new paper being discussed on this thread confirms that the SE Asian P* and MPS is far distant from MA1's pre-R):


MA-1 (Y-preR) is perhaps separated by about 20000 years form the Sunda type (Y-MP) and represents a small subset of SE Asian M526 diversity. Modern Papuans are separated by about 45000 from the Sunda Y-MP so a total separation of about 65000 between MA-1 and the early Sunda type (when compared to MA-1's upper Eurasian and American descendants who are separated by 24000years).

http://www.anthrogenica.com/showthread.php?1781-Post-Your-EEF-WHG-and-ANE-Admixture-Proportions/page26

parasar
06-19-2014, 01:09 AM
Do you have direct evidence for that? I hope so? He had mtdna hg R and that is verified. http://snag.gy/IzthP.jpg

Any idea what kind of R? Tianyuan was an R derivative of B4'5 type. Tianyuan who had been estimated to be equidistant to almost every modern population except Africans, has an mtDNA type that most likely originated in far E Asia.

http://en.wikipedia.org/wiki/Haplogroup_R_(mtDNA)

R11'B (16189)
R11: Found in China, mainly in Lahu people from Yunnan at 12.5%.[22] Also in Japan and Rajasthan (India).
B
B4: It is found often in East Asia, Southeast Asia, Polynesia, Melanesia, Micronesia, Madagascar and Indigenous peoples of the Americas.
B5: Spread in East Asia and Southeast Asia.
R24: Found in Philippines.[23]


Haplogroups R11'B6 and B4'B5.
Haplogroup B is found at relatively high frequencies in Mainland southeastern Asia (20.6%), Island southeastern Asia (15.5%), Oceania (10.2%), eastern Asia (10.5%) and America (24%), but occurs as rarely as 0.1–1% in the Volga-Ural region, the Caucasus, western and southern Asia. It is detected at a very low frequency in some populations of Europe. Haplogroup B is found at ~3% overall in northern and central Asia, although it reaches >10% in a few Siberian populations...
The relatively large amount of internal variation accumulated in the northern Asian branch of B4b1a would mean that B4b1a3 arose in situ in southern Siberia after the arrival of B4b1a3 founder mtDNA from somewhere else in eastern Asia. The phylogeny depicted in Figure S1 provides additional information concerning the entry time of the founder mtDNA - the age of B4b1a3 node is estimated as ~18–20 kya using different mutation rates, thus pointing to a pre-LGM/LGM

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032179

Both of these - Ust Ishim and Tianyan - are consistent with age of YAP insertion of over 40000years.

aarnisotka
06-19-2014, 06:57 AM
No. I had seen that tweet, and mtDNA R would point to the east Asian side, but I'm not able to figure out how the autosomal evidence is showing clearly OOA, that was the reason for the YAP guess.
https://pbs.twimg.com/media/Bpsmqs8CYAARPV3.jpg

I reckon the clear OOA could just mean that it's a very pure OOA, in other words lacking the SSA affinities and admixtures of it's descendants.

vettor
06-21-2014, 12:27 AM
Can anyone tell me where the origin of K was...........pamir mountains or Gedrosia ?

vettor
10-04-2014, 08:35 PM
The new breakup of K ydna group ( 1st of october 2014)

http://www.isogg.org/tree/ISOGG_HapgrpK.html

maybe I can classify myself now, as K1b-L446:biggrin1:

VinceT
10-05-2014, 02:15 AM
I pity the guys who now belong to haplogroup K2b2a2a2a1b1a1a3b2b1a1a2b1a1. :P

ChrisR
10-16-2014, 11:47 AM
Dienekes has the following image:

http://3.bp.blogspot.com/-W9tCYUPoeDo/U4_75fH8RPI/AAAAAAAAJnk/PeGLt4vWhk4/s1600/K-M526.png

From what I recall of the earlier study they didn't have a sample from a Haplogroup S man, so it's position wasn't known. Obvioulsy what's termed P331 in the above diagram is what was provisionally classed "MP", if they had a Haplogroup S sample back then they probably would have called it "MPS" (Aka. K2b)

-Paul
(DF41+)
Is the article available and/or have they mentioned equivalent SNPs? (I have not chewed trough the whole thread)

vettor
10-16-2014, 05:20 PM
Is the article available and/or have they mentioned equivalent SNPs? (I have not chewed trough the whole thread)

as per link below ( bottom in the link) a new X ydna has been indroduced in June 2014 to sit as part of K2a
http://en.wikipedia.org/wiki/Paragroup

Kale
05-20-2015, 05:55 PM
I'm not advocating any side of the debate here...but how do the proponents of a Southeast Asian origin of K2 reconcile Ust-Ishim with their theory?

Megalophias
05-20-2015, 07:57 PM
I'm not advocating any side of the debate here...but how do the proponents of a Southeast Asian origin of K2 reconcile Ust-Ishim with their theory?

Not advocating any side either, but K2 probably originated ~5000 years before Ust'-Ishim man, which is plenty of time to reach Siberia.

Kale
05-21-2015, 12:46 PM
Not advocating any side either, but K2 probably originated ~5000 years before Ust'-Ishim man, which is plenty of time to reach Siberia.

Yes, but if Ust-Ishim came from Southeast Asia, shouldn't he be closer to Southeast Asians autosomally? He seems ancestral to everybody except Middle Easterners and Africans.

Was he an early unsuccessful adventurer north? With the K2 descendants we see today not expanding for at least a few thousand years after?

yxc
05-21-2015, 04:26 PM
Ust-Ishim came from where IJK later K1 and K2 just had bifurcated according to molecular clock estimates.

it's not my business to make any further exact claims where and when .

Megalophias
05-21-2015, 10:39 PM
Yes, but if Ust-Ishim came from Southeast Asia, shouldn't he be closer to Southeast Asians autosomally? He seems ancestral to everybody except Middle Easterners and Africans.

Was he an early unsuccessful adventurer north? With the K2 descendants we see today not expanding for at least a few thousand years after?

It's really hard to tell who if anyone he is closer to, because Denisovan and basal Eurasian admixture throws things off - and sheer noise:

Yoruba, Ust_Ishim; Atayal, Han +0.0025 +1.106
Yoruba, Ust_Ishim; Ami, Han -0.0036 -1.91

(unless this is differential admixture with Taiwanese pygmies or something!)

Anyway, he carries both Y hg K and mtDNA R. So whether or not his particular population were successful, his not-too-distant relatives certainly were, and they spread closely related ancestry all over the world.

parasar
01-20-2017, 05:31 PM
Sundaland is supposedly the partly sunken SE Asian subcontinent, main remnants of which are the islands west of Wallace's line.
While I agree with most of Maju's analysis, if you look at Poznik's phylogeny and timeline, F-M89 to K-M526 is fast.
I doubt any long distance migration could have occurred in such a short period. Therefore I am of the opinion that F-M89 was itself a Sunda line.
...



A new paper on this:
"Given functionality for genome wide autosomal SNPs as discussed above, it is easily
inferred that most SNPs in Y chr are also non-neutral. We therefore redrew the Y tree based on
shared alleles, which may mean common physiology more than common adaptations if
physiology is the chief determinant of MGD. Using 58251 cleanly called SNPs (no individual
with uncalled SNPs, Supplementary Table S9) and previously defined haplotypes for 1kGP
samples (Poznik et al., 2016), we found a major megahaplogroup ABCDE (Figure 2).
Megahaplotype F, defined as lacking any mutations that define other haplotypes, is the ancestor.
All F-like or F* haplotypes sequenced so far are partial ABCDE carrying 4 (Lahu_HGDP01320),
13 (Malay_SSM072) or 14 (KHV_HG02040) of the 151 mutations that group ABCDE (Figure 2)
(Karmin et al., 2015; Mallick et al., 2016; Poznik et al., 2016). The F* haplotype is most common
in East Asia, present in 5 of 7 (71.4%) Lahu males in Yunnan of South West China (Black et al.,
2006), 10-15% of Han and other minority Chinese, and low percentages (<10%) in South
Asians and French. Furthermore, the top 4 individuals among 1kGP closest to the ~45,000 year
old Western Siberian Ust’-Ishim who carried NO haplotype and was expected to be most like
the AMH ancestor were all East Asians with Asian haplotypes F and O (F2 in KHV_HG02040,
O2 in CHB_NA18534, O3 in CHS_HG00559, O3 in KHV_HG02088), indicating least deviation
from the ancestor for Asian haplotypes (Fu et al., 2014). These three O type East Asian
individuals also were the closest to the three F* carrying individuals above. These results
suggest the origin of F in East Asia with subsequent migration to other regions of the world
(Supplementary Figure S3)."
http://biorxiv.org/content/biorxiv/early/2017/01/18/101410.full.pdf

kinman
03-04-2017, 03:51 AM
I have just begun looking at Haplogroup K and its descendants. I am particularly interested in the origin of Haplogroup P.
Although Luzon is apparently the only location where P*, P1* and rare P2 are now found together (plus significant levels of K2b1), does that necessarily mean that there was a very long westward back-migration before giving rise to Haplogroups Q and R?
Is it possible Haplogroup P originated in some place like India, and that it is a just an historic fluke that Luzon is now where so many primitive members now reside together? Something like a widespread Haplogroup P (from India to Philippines) and then massive replacement of Haplogroup P men in between by other haplogroups)? Perhaps there was once P*, P1* and rare P2 found together in India as well?

Kale
03-04-2017, 06:11 AM
y-hg replacement seems to be the rule rather than the exception. I think certain environments tend to preserve diversity better however, such as those that lend themselves to possessing many small groups of people who have contact only with their neighbors. (I think jungle and maybe islands would fit that)

ataneojr1
02-22-2018, 10:39 PM
just got my FTDNA Y12 and it says Confirmed K-M9 Ydna Haplogroup???

ataneojr1
02-25-2018, 01:34 AM
It's really hard to tell who if anyone he is closer to, because Denisovan and basal Eurasian admixture throws things off - and sheer noise:

Yoruba, Ust_Ishim; Atayal, Han +0.0025 +1.106
Yoruba, Ust_Ishim; Ami, Han -0.0036 -1.91

(unless this is differential admixture with Taiwanese pygmies or something!)

Anyway, he carries both Y hg K and mtDNA R. So whether or not his particular population were successful, his not-too-distant relatives certainly were, and they spread closely related ancestry all over the world.

I am Filipino and I share One DNA Segment with Ust-Ishim at 50 SNP and 7Cm. Gedmatch using Ust Ishim kit number One on One

vettor
02-25-2018, 02:26 AM
I have just begun looking at Haplogroup K and its descendants. I am particularly interested in the origin of Haplogroup P.
Although Luzon is apparently the only location where P*, P1* and rare P2 are now found together (plus significant levels of K2b1), does that necessarily mean that there was a very long westward back-migration before giving rise to Haplogroups Q and R?
Is it possible Haplogroup P originated in some place like India, and that it is a just an historic fluke that Luzon is now where so many primitive members now reside together? Something like a widespread Haplogroup P (from India to Philippines) and then massive replacement of Haplogroup P men in between by other haplogroups)? Perhaps there was once P*, P1* and rare P2 found together in India as well?

correct me if I am wrong , but did karafet state K created in modern "burma" area ..........was it the 2014 or 2015 paper?

BMG
03-01-2018, 04:58 PM
There is another indian in pre-NO K-M2335 in Yfull.tree . The present sample from Kerala doesn't belong to the subgroup the two samples belong to .