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Krefter
10-17-2015, 09:51 AM
Remember: By basal R, I mean any R that is not R1a1a1-M417 and R1b1a2a-L23, because those lineages take up 90%+ of R today. Looking at R(xL23, M417) can help learn about the origins of L23 and M417.

I'm going to use this thread as....

>An option for people to post information/discuss about basal clades of Y DNA hg R.
>For myself to post any information I find on basal clades of Y DNA hg R. I'm going to make a Y DNA Atlas blog to put as much Y DNA data as possible, like I did for mtDNA.

Among members here and even some academics it's unanimously believed that both R1a1a1-M417 and R1b1a2a-L23 were carried mostly by early Indo European speakers and expanded out of Russia/Ukraine starting in circa 3000 BC. Arguments nowadays revolve around where the ancestors of R1a1a1-M417 and R1b1a2a-L23 came from. Some of the best evidence you can give for an origin is diversity of R(xL23, M417). The R1b1 and R1a1 from Mesolithic Russia are dead-lineages. IMO, there's a high possibility both M417 and L23 are from West Asia.

Here's some data I've gathered from online sources. I only have data from Near East, Caucasus, Iran, SC Asia, East Europe, and Sweden so far. Not all samples were tested at the same coverage.

Basal R frequencies (https://docs.google.com/spreadsheets/d/1uFFYxChF4rnfBWFZhhuyRE_Jm-8VXGPwiE5XO2OV_JA/edit#gid=0)


The string of R*(xR1, R2a) in Asia should be ignored because it is probably R2(xR2a), some might be R* who knows. There's a single R(xR1) from East Finland which might be R*. The only legitimate R* is a single sample from Kyrgz(Central Asia), it was negative for R1 and R2. The only R1, that is negative for basal forms of R1a and R1b, are from Oman in SW Arabia, Pakistan, Iran, and Ukraine(xR1a1a, R1b1a, could be R1b1c). Early forms of R1 are absent from Caucasus, India, SC Asia.

2.7% of Iran Y DNA is of Basal forms of R1, R1b, and R1a1. And it's spread-out and not restricted to one of the three. You don't see this anywhere else in Asia and not in East Europe. The only other locations basal forms of R1, R1a, and R1b are found that are probably not R1b1c/R1b1a1 is in Pakistan(R1, xR1a1a, R1b1), NW Caucasus(R1a1, xR1a1a), and Ukraine(R1, xR1b1a, R1a1a). I have very little data, I think most importantly from Volga/Ural Russia and North Asia, but with what I have R1, R1a, and R1b basal forms are most popular in Iran.

Gravetto-Danubian
10-17-2015, 09:58 AM
This is a good start

https://www.familytreedna.com/groups/ht-3-5new/about/background

rms2
10-17-2015, 03:33 PM
The problem with the term "basal" is that it is being applied to modern men who certainly do not belong to clades that are truly basal but merely to little-studied clades for whom no string of terminal SNPs is yet known. Modern men are modern men, after all, not throwbacks to some bygone era. I think one has to look not to odd one-offs here or there but to where the major splits seem to have occurred. Better yet is to look at where the oldest ancient y-dna is showing up.

Of course, the fact that these small "basal" results are showing up in Asia is no surprise really, since that is where the member clades of Super Group K are found all within relatively close proximity to one another.

I think Mal'ta Boy turning up in Siberia near Lake Baikal is an important clue.

George
10-17-2015, 04:09 PM
"The R1b1 and R1a1 from Mesolithic Russia are dead-lineages. IMO, there's a high possibility both M417 and L23 are from West Asia."

The Karelian guy is only ancestral to M417. But I don't read Haak as ruling out the possibility of M417 also originating in that general area. I'm not sure whether the R1a's from Serteya have been fully analyzed or not. So unless you have some very good reason (other than a lack of data), excluding the territories north and west of Khvalynsk as potential R1a-M417 seems premature. There's been hardly any testing.

DMXX
10-17-2015, 04:10 PM
If you haven't already Krefter, check out Di Cristafaro et al.'s data for Central Asia (including Afghanistan). Some interesting Y-DNA R parahaplogroups emerged there. You could also check Arunkumar et al. for any South Indian R parahaplogroups, or the several SNP-confirmed papers done on Pashtun Y-DNA since 2012. I wouldn't bother using STR-only papers for this purpose (parahaplogroups behave strangely in subclade predictors for obvious reasons).

The standard caveat regarding the fallacy of assuming modern population distributions can be reverse-transposed onto the past. The directional nature of time means the past generally explains the present and not vice versa.

In the case of Iran, it's been apparent to me for some years that the Iranian plateau (and adjacent regions) are currently particularly rich in Y-DNA R parahaplogroups (my own R2a-M124 appears to be one of these for now).

One possibility I anticipate may emerge is the derivation of early Y-DNA R1 across the steppes via HG's, with a few wayward branches happening to reach places like Iran, Afghanistan or Tajikistan in prehistoric times. Some of these lines may well have remained further north in Central Asia and then brought into these regions by European steppe derived populations.

There's several explanations accounting for the Iranian R parahaplogroups which don't require an actual origin in Iran. At face value, their presence does not immediately agree with the aDNA we have so far (Mal'ta, various Neolithic and Mesolithic European steppe results). Some have proceeded to conclude the European steppe is the cradle of all things Y-DNA R1. In the absence of West Asian aDNA and the lack of an empirical explanation regarding the Iranian-Central Asian Y-DNA R parahaplogroup situation, that is a premature conclusion. There is no rational argument in favour of crystallising this view at present ("absence of evidence isn't evidence of absence" alone determines this).

Having said that, the convenience of Y-DNA R* (Mal'ta), R1a* (Karelian HG), R1b* (Samara HG) and several R1a and R1b subclades residing on the steppes clearly makes this the favoured working scenario for now. All options are on the table until we have more data.

Coldmountains
10-17-2015, 04:32 PM
The problem with the term "basal" is that it is being applied to modern men who certainly do not belong to clades that are truly basal but merely to little-studied clades for whom no string of terminal SNPs is yet known. Modern men are modern men, after all, not throwbacks to some bygone era. I think one has to look not to odd one-offs here or there but to where the major splits seem to have occurred. Better yet is to look at where the oldest ancient y-dna is showing up.

Of course, the fact that these small "basal" results are showing up in Asia is no surprise really, since that is where the member clades of Super Group K are found all within relatively close proximity to one another.

I think Mal'ta Boy turning up in Siberia near Lake Baikal is an important clue.

I agree. The basal R1 branches in Iran for example are not proving much and I don't see how R1a-M417 or R1b is from West Asia especially when R1b and R1a were the dominant markers of EHG which were genetically between WHGs and ANEs so just an East European or maybe West Siberian origin makes sense for these PIE clades of R1a and R1b. We don't need to make it more complicated than it is is and R1 is obviously from Siberia/ the mammoth steppe.

rms2
10-17-2015, 04:38 PM
. . . The directional nature of time means the past generally explains the present and not vice versa . . .


Super quotable line! One of the best I've seen in a long while. I'll probably plagiarize it frequently.

DMXX
10-17-2015, 04:44 PM
I agree. The basal R1 branches in Iran for example are not proving much and I don't see how R1a-M417 or R1b is from West Asia especially when R1b and R1a were the dominant markers of EHG which were genetically between WHGs and ANEs so just an East European or maybe West Siberian origin makes sense for these PIE clades of R1a and R1b. We don't need to make it more complicated than it is is and R1 is obviously from Siberia/ the mammoth steppe.

Autosomal component associations aren't reliable.

Before the aDNA era, some users on another forum found there was a "positive correlation" between the "Mediterranean" component of several ADMIXTURE calculators with R1b-M269.

The conclusion was made that R1b-M269 was brought into Europe via a different, more "southerly" route than R1a-M17. A year into the aDNA era, I don't think that's even a minority view right now, even if some circles were firm proponents of it.

For the sake of preventing another "house of cards" scenario, we'd be better off ignoring auDNA associations and focus squarely on SNP-guided MRCA calculations using a combination of ancient and modern samples.

This is a matter of uniparental phylogeny, after all. What better way to answer Y-DNA questions than with Y-DNA data?

Megalophias
10-17-2015, 04:58 PM
The problem with the term "basal" is that it is being applied to modern men who certainly do not belong to clades that are truly basal but merely to little-studied clades for whom no string of terminal SNPs is yet known.
"Basal" means it branched off before the main clade. It doesn't mean it is frozen in time. This is normal biological usage, e.g. one can refer to sea squirts as basal chordates, even though they are modern species that split from vertebrates many hundreds of millions of years ago.

So no, this is perfectly correct usage, and the clades are truly basal. If some people are confused and think "basal" means "ancestral and unchanged", then educate them.

Coldmountains
10-17-2015, 05:00 PM
Autosomal component associations aren't reliable.

Before the aDNA era, some users on another forum found there was a "positive correlation" between the "Mediterranean" component of several ADMIXTURE calculators with R1b-M269.

The conclusion was made that R1b-M269 was brought into Europe via a different, more "southerly" route than R1a-M17. A year into the aDNA era, I don't think that's even a minority view right now, even if some circles were firm proponents of it.

For the sake of preventing another "house of cards" scenario, we'd be better off ignoring auDNA associations and focus squarely on SNP-guided MRCA calculations using a combination of ancient and modern samples.

This is a matter of uniparental phylogeny, after all. What better way to answer Y-DNA questions than with Y-DNA data?

Yes but I am talking about Mesolithic/Neolithic autosomal and Y-DNA , which is quite good correlating to each other. EHGs and Neolithic Farmers had totally different autosomal and Y-DNA for example but today autosomal and Y-DNA is not so good correlating with each other among modern populations. Ancient populations were genetically more homogeneous and their Y-DNA was often closely linked to their autosomal DNA (but of course not in every case).In the case of steppe R1b/R1a we see that EHG males lacking West Asian ancestry belonged to the same haplogroups and that later with the arrival of "teal" autosomal and mtdna PIEs became West Asian shifted so it is very unlikely that PIEs got their R1 from West Asia. But some R1 entering West Asia from the EHG steppe or Central Asia could of course very early exist there.

Megalophias
10-17-2015, 05:52 PM
. I have very little data, I think most importantly from Volga/Ural Russia and North Asia, but with what I have R1, R1a, and R1b basal forms are most popular in Iran.
I think the biggest holes in the data are North Central Asia and South Asia. There is all kinds of crazy stuff in North Central Asia but because of the tendency to tribal founder effects sampling one or two populations will get you a whole lot of one common haplogroup and not much of the rarer stuff. Like with Kazakhs, where one study finds they are massively G1, another they are mostly R1a, another they'll be mainly C2b. The same thing happens in South Asia because the groups are endogamous, and there are over a billion inhabitants, it is ludicrously undersampled.

Most studies are not resolved below M269, so it is hard to tell whether it is L23 or not. For M269(xL23) the only unusual element of distribution I can think of is that it is present in North Africa at higher level than in most of Europe or West Asia (3/297 according to Bekada).

Since you have all the West Eurasian data I do, here is South and East Asia:

Tibet: 4/2354 R1b-M343(xM335, M73, M269), I'd guess R1b-PH1165; also 2/2354 R1b-M73; no M269 at all; 1/2354 R1*(xR1b-M343, R1a1a-M17) - could be basal R1a.
Ladakh (Kashmir region): 1/215 R1b-M335; 1/215 R1a1*-SRY1532(xR1a1a-M17).
India: 2/1152 R1a1*-SRY1532(xR1a1a-M17) (1 upper caste North Indian, 1 Munda tribal); 13/1152 R1*-M173(xR1a1-SRY1532, R1b1a2-M269) - mostly in low-middle caste Dravidian speakers from South India. (Trivedi 2007, pretty old and maybe not that reliable).
Bali: 2/641 R1b1-P25(xM269) - Bali has a lot of Indian Y DNA so could be from there
Southern China: 1/447 Yunnanese had R1b-M335 (Hua Zhong et al 2011);
Northern China: 3/853 Northern Han R1b-M73 (all from Gansu, which is quite far in the northwest); 1/853 R1b*-M343 (xM269, M73, M335) - from Shandong, in the east.

There is very, very little properly tested data from South Asia.

No frequency data available, but R1b-PH1165, the most basal form, is reported in a Tajik and a Bhutanese, and from private testing probably also in 2 Indians and a Uyghur from Xinjiang.

rms2
10-17-2015, 07:18 PM
"Basal" means it branched off before the main clade. It doesn't mean it is frozen in time. This is normal biological usage, e.g. one can refer to sea squirts as basal chordates, even though they are modern species that split from vertebrates many hundreds of millions of years ago.

So no, this is perfectly correct usage, and the clades are truly basal. If some people are confused and think "basal" means "ancestral and unchanged", then educate them.

Thanks, but I guess then "basal" in the case of y-dna depends on whose clade is considered the "main clade". I see it constantly used as if it should be regarded as representing throwbacks frozen in time who allow us to pinpoint the birthplace of the y haplogroup.

Krefter
10-17-2015, 08:41 PM
For the sake of preventing another "house of cards" scenario, we'd be better off ignoring auDNA associations and focus squarely on SNP-guided MRCA calculations using a combination of ancient and modern samples.


I agree that's sometimes the case. But with EHG they had a high frequency of multiple basal R1as and R1bs and even Q1a. Modern SW Euros have a lot of R1b because of a single young founder effect, that wasn't the case for EHG with R1a/R1b/Q. So, an argument for an autosomal connection between them and R1 is not as unvalid and old arguments for West Mediterranean origin.


.....I think one has to look not to odd one-offs here or there but to where the major splits seem to have occurred. Better yet is to look at where the oldest ancient y-dna is showing up.

Of course, the fact that these small "basal" results are showing up in Asia is no surprise really, since that is where the member clades of Super Group K are found all within relatively close proximity to one another.

I think Mal'ta Boy turning up in Siberia near Lake Baikal is an important clue.

Good point. I don't think R1 diversity in Iran means R1 originated there or that R1a1a1 and R1b1a2a orignated there. It's evidence that's the case, but there could be many differnt reasons it is the case. It's shocking that EHG was mostly of basal R1b and R1a, such a situation could not have been predicted with modern data.


I think the biggest holes in the data are North Central Asia and South Asia. There is all kinds of crazy stuff in North Central Asia but because of the tendency to tribal founder effects sampling one or two populations will get you a whole lot of one common haplogroup and not much of the rarer stuff. Like with Kazakhs, where one study finds they are massively G1, another they are mostly R1a, another they'll be mainly C2b. The same thing happens in South Asia because the groups are endogamous, and there are over a billion inhabitants, it is ludicrously undersampled.

Most studies are not resolved below M269, so it is hard to tell whether it is L23 or not. For M269(xL23) the only unusual element of distribution I can think of is that it is present in North Africa at higher level than in most of Europe or West Asia (3/297 according to Bekada).

Since you have all the West Eurasian data I do, here is South and East Asia:

Tibet: 4/2354 R1b-M343(xM335, M73, M269), I'd guess R1b-PH1165; also 2/2354 R1b-M73; no M269 at all; 1/2354 R1*(xR1b-M343, R1a1a-M17) - could be basal R1a.
Ladakh (Kashmir region): 1/215 R1b-M335; 1/215 R1a1*-SRY1532(xR1a1a-M17).
India: 2/1152 R1a1*-SRY1532(xR1a1a-M17) (1 upper caste North Indian, 1 Munda tribal); 13/1152 R1*-M173(xR1a1-SRY1532, R1b1a2-M269) - mostly in low-middle caste Dravidian speakers from South India. (Trivedi 2007, pretty old and maybe not that reliable).
Bali: 2/641 R1b1-P25(xM269) - Bali has a lot of Indian Y DNA so could be from there
Southern China: 1/447 Yunnanese had R1b-M335 (Hua Zhong et al 2011);
Northern China: 3/853 Northern Han R1b-M73 (all from Gansu, which is quite far in the northwest); 1/853 R1b*-M343 (xM269, M73, M335) - from Shandong, in the east.

There is very, very little properly tested data from South Asia.

No frequency data available, but R1b-PH1165, the most basal form, is reported in a Tajik and a Bhutanese, and from private testing probably also in 2 Indians and a Uyghur from Xinjiang.

Thanks for the data. So R1b in Tibet is of a differnt variety than other R1b. Was there anyother R1 from South/North China? Can you reference the studies you get this data from?

Megalophias
10-17-2015, 09:54 PM
- Hua Zhong et al 2011, "Extended Y-chromosome investigation suggests post-Glacial migrations of modern humans into East Asia via the northern route." - A large sample plus pooled data from the literature focussing on exotic/West Eurasian Y haplogroups in China (i.e. not C, D, N, and O).
- Xuebin Qi et al 2013, "Genetic Evidence of Paleolithic Colonization and Neolithic Expansion of Modern Humans on the Tibetan Plateau". - Very large sample size from all across Tibet, with a good number of SNPs tested.
- Sahoo et al 2006, "A prehistory of Indian Y Chromosome: Evaluating demic diffusion scenarios". This study was extended with more data and published by Trivedi as a book chapter, apparently:
High Resolution Phylogeographic Map of Y-Chromosomes Reveal the Genetic Signatures of Pleistocene Origin of Indian Populations (http://www.krepublishers.com/06-Special%20Volume-Journal/T-Anth-00-Special%20Volumes/T-Anth-SI-03-Anth-Today-Web/Anth-SI-03-31-Trivedi-R/Anth-SI-03-31-Trivedi-R-Tt.pdf). It is really old but has yet to be superseded by a decent large-scale study of Indian Y-chromosomes, which is kind of crazy.
- Rowold et al 2015, "Ladakh, India: the land of high passes and genetic heterogeneity reveals a confluence of migrations". - Came out very recently.
- Karafet et al 2010, "Major East–West Division Underlies Y Chromosome Stratification across Indonesia". - A pretty good survey of Indonesia.

Krefter
10-19-2015, 05:21 AM
R1a1a(xZ93, Z282) is consistently popping up in Volga Ural. My guess is most is of unknown R1a-M417, R1a-Z93, or R1a-Z283 basal clades.

http://www.forumbiodiversity.com/showthread.php/43792-Haplogroup-composition-of-the-populations-from-the-Volga-Ural-region-(Trofimova-2015)

kinman
10-20-2015, 04:02 PM
One basal clade on YFull that has long puzzled me is R-L389* (id: HG00640). If it was somebody from Kazakhstan, Russia, or Ukraine, it wouldn't be so puzzling---but Puerto Rico. Very strange.

--------------Ken

Megalophias
10-20-2015, 05:24 PM
One basal clade on YFull that has long puzzled me is R-L389* (id: HG00640). If it was somebody from Kazakhstan, Russia, or Ukraine, it wouldn't be so puzzling---but Puerto Rico. Very strange.
It is also found in Italians, Armenians, and various other Mediterranean/West Asian people.

Consider the distribution of R1b-V88, and it shouldn't be surprising to find upstream R1b clades in far flung places (Puerto Ricans being mainly descended paternally from South Europeans with a little West African). It is P297 that is associated with the steppe, not all of R1b.

kinman
10-20-2015, 05:54 PM
Yes, but this is L389* (with an asterisk). Doesn't that mean he tested negative for all downstream SNPs? I would think such a person would usually be closer to where L389 originated. YFull does not list anyone under R-V88* (with an asterisk), but if they did, I would expect him to be from some place like Saudi Arabia (not Africa).
---------------Ken
P.S. I couldn't find L389 listed at ISOGG (either in the tree or the SNP index).
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It is also found in Italians, Armenians, and various other Mediterranean/West Asian people.

Consider the distribution of R1b-V88, and it shouldn't be surprising to find upstream R1b clades in far flung places (Puerto Ricans being mainly descended paternally from South Europeans with a little West African). It is P297 that is associated with the steppe, not all of R1b.

Megalophias
10-20-2015, 06:44 PM
Yes, but this is L389* (with an asterisk). Doesn't that mean he tested negative for all downstream SNPs? I would think such a person would usually be closer to where L389 originated. YFull does not list anyone under R-V88* (with an asterisk), but if they did, I would expect him to be from some place like Saudi Arabia (not Africa).
---------------Ken
P.S. I couldn't find L389 listed at ISOGG (either in the tree or the SNP index).

L389 is just one of the SNPs in the block between the branching off of V88 and the P297 node, unless you have a rare L389(xP297) sample. I have never seen L389* in an academic study, only in private testing.
We don't know where L389 originated, very little is known of upstream R1b. I would guess L389* is a sister branch of P297 from the Near East originally, though Gioiello will inform you that all R1b below L754 is from Italy. :) Keep in mind that testing of Y DNA globally is very uneven, someone happened to decide to test a bunch of Puerto Ricans, so that's where it was found. Maybe you could test some random village in Iraq and they'd all be L389*, who knows.

alan
10-20-2015, 08:29 PM
I agree that's sometimes the case. But with EHG they had a high frequency of multiple basal R1as and R1bs and even Q1a. Modern SW Euros have a lot of R1b because of a single young founder effect, that wasn't the case for EHG with R1a/R1b/Q. So, an argument for an autosomal connection between them and R1 is not as unvalid and old arguments for West Mediterranean origin.



Good point. I don't think R1 diversity in Iran means R1 originated there or that R1a1a1 and R1b1a2a orignated there. It's evidence that's the case, but there could be many differnt reasons it is the case. It's shocking that EHG was mostly of basal R1b and R1a, such a situation could not have been predicted with modern data.



Thanks for the data. So R1b in Tibet is of a differnt variety than other R1b. Was there anyother R1 from South/North China? Can you reference the studies you get this data from?

I think whatever distribution patterns were present in north Euroasia at the start of the LGM like R* and early derivatives were probably radically altered by the LGM followed by a period of forest covering the area then hit again by the shock of the late cold snap in the Younger Dryas returning glacial type conditions and then reforestation in the Boreal. I cant see any distribution patterns of R or even earliest R1, R1b and R1a having survived all that. The clearest demonstration is that we know an early R was present in Baikal c. 22000BC and in all probability across south-central Siberia for much of 30000-22000BC (the chronological/geographical description of the culture of Mal'ta boy) and yet there are few if any basals in that area today. When you consider the shocking climatic oscillations I just discussed in very simplified terms above, this is not surprising.

kinman
10-20-2015, 09:09 PM
Doesn't L389* (with the asterisk) indicate that this is a rare L389(xP297)? And if I'm reading YFull's tree correctly, the small block between V88 and the P297 node only seems to have 2 SNPs: L389/PF6531 and L388/PF6468.
I looked at the R1b and Subclades Project, and I could only find two people listed as having L389 as their terminal SNP (one from Italy and one from Greece). But do we know for sure that they are P297 negative? And where can one find the results of the Armenians and West Asians who are L389? Something just doesn't feel right, and I'm just trying to understand why.
------------Ken
----------------------------------------------------------------------------------------------------------------


L389 is just one of the SNPs in the block between the branching off of V88 and the P297 node, unless you have a rare L389(xP297) sample. I have never seen L389* in an academic study, only in private testing.
We don't know where L389 originated, very little is known of upstream R1b. I would guess L389* is a sister branch of P297 from the Near East originally, though Gioiello will inform you that all R1b below L754 is from Italy. :) Keep in mind that testing of Y DNA globally is very uneven, someone happened to decide to test a bunch of Puerto Ricans, so that's where it was found. Maybe you could test some random village in Iraq and they'd all be L389*, who knows.

lgmayka
10-20-2015, 09:56 PM
One basal clade on YFull that has long puzzled me is R-L389* (id: HG00640). If it was somebody from Kazakhstan, Russia, or Ukraine, it wouldn't be so puzzling---but Puerto Rico.
That Puerto Rican lineage diverged from (what became) R-P297 about 15,800 years ago (http://yfull.com/tree/R-L389/). Interestingly, that is just the right timeframe for expansion into the Americas. (Native American Q-M3 diverged from European Q-L804 about 15,000 years ago (http://yfull.com/tree/Q-M930/), and Native American Q-Z780 diverged from the rest of Q about 15,600 years ago (http://yfull.com/tree/Q-Z780/).)

Perhaps this R-L389* guy tagged along with the Q men. :) If I were looking for remnants of a haplogroup that had otherwise died out in the Americas, I would certainly check islands.

Huntergatherer1066
10-20-2015, 10:06 PM
https://www.familytreedna.com/public/R1b1Asterisk/

You can see a number of examples of L389+ P297- people in Cluster A of this project, they're in the R-PF4354+ branch on the FTDNA tree.

Gravetto-Danubian
10-20-2015, 11:04 PM
It is P297 that is associated with the steppe, not all of R1b.

Indeed, although I have got the feeling that many would have all R1b –M343 originating in / expanded from the steppe or Siberia - which is not possible given the peri-Glacial settlement history of the regions. Moreover, some even have V88 as an early forager off-shoot drifting south and moving along with Neolithic farmers. This always sounded unlikely to me.

To me, the real question is did M297 'evolve' on the steppe from P25*, or did it arrive from further southeast as one block, or even as 2 successive waves – first M73, then M269 ?

kinman
10-21-2015, 12:16 AM
Thanks Huntergatherer1066,
I see that FTDNA actually has PF4354 in two different places in their tree. So I assume that this one is PF4354.1 , and that PF4354.2 is the one nested down within DF27, Z195, etc.
Therefore, is PF4354 what is called a "floating SNP"?

-------------Ken
---------------------------------------------------------------------------------------------------------------------


https://www.familytreedna.com/public/R1b1Asterisk/

You can see a number of examples of L389+ P297- people in Cluster A of this project, they're in the R-PF4354+ branch on the FTDNA tree.

Huntergatherer1066
10-21-2015, 12:50 AM
Thanks Huntergatherer1066,
I see that FTDNA actually has PF4354 in two different places in their tree. So I assume that this one is PF4354.1 , and that PF4354.2 is the one nested down within DF27, Z195, etc.
Therefore, is PF4354 what is called a "floating SNP"?

-------------Ken
---------------------------------------------------------------------------------------------------------------------

That's correct, it is recurrent. The two samples in that project that positive for it are negative for P297 and its equivalents. Neither of them are the Puerto Rican YFull sample though. Ideally this subclade would have a different name, when another equivalent SNP that is not recurrent is found.

kinman
10-22-2015, 02:31 AM
What is your source concerning the peri-Glacial settlement history of the steppe and Siberia (which you claim makes it not possible for R1b to have originated there)? That is a huge area.

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Indeed, although I have got the feeling that many would have all R1b –M343 originating in / expanded from the steppe or Siberia - which is not possible given the peri-Glacial settlement history of the regions. Moreover, some even have V88 as an early forager off-shoot drifting south and moving along with Neolithic farmers. This always sounded unlikely to me.

To me, the real question is did M297 'evolve' on the steppe from P25*, or did it arrive from further southeast as one block, or even as 2 successive waves – first M73, then M269 ?

Gravetto-Danubian
10-22-2015, 03:38 AM
What is your source concerning the peri-Glacial settlement history of the steppe and Siberia (which you claim makes it not possible for R1b to have originated there)? That is a huge area.

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Hi KM
Yes it is a big area; but it was a big empty area between 22-16000 BC. I don't have the time to look up and list an extensive reference base, but you can see "The Eastern Gravettian “Kostenki Culture” as an Arctic adaptation" by John hoffecker (which shows that Russian plain was depopulated) and "Modern Human Colonization of the Siberian Mammoth Steppe: A View from South-Central Siberia" by Graf (where she bunks older arguements that Siberia was continuously populated during the LGM) . Also note that mal'ta was the "last of his kind" in Siberia ; although the met-population from which he derived survived to later contribute to EHG and Americans . So where was this refuge ? Possibly the Altai ; where there is a continuous typology of micro blade development (but no human or settlement evidence); or possibly anywhere in southern Central Asia which was warmer but modern research is still at a poor stage

I have no personal investment as to where r1b as a whole originated from, but the above settlement evidence combined with modern phylogeny of two branches parallels (V88, M343) to M297 suggestive of an epicentre somewhere south of the Caucasus makes the idea of M343 originating in the steppe non-parsimonious, but certainly not impossible given the caution we must exercise when analysing through the veil of modern patterns , and what we know about the dynamic character of human settlement / demography in general

kinman
10-23-2015, 12:13 AM
Sorry but the paper by Graf does NOT debunk older arguments that Siberia was continuously populated during the LGM. The population was low, as one would expect. Graf says: "At about 24,000 cal BP, populations in southcentral Siberia dwindled to archaeologically unrecognizable levels. Whether or not humans completely disappeared from Siberia during the LGM is not known; however, in the Enisei River basin populations seemed to have been quite low."

This does not sound like a "big empty area" as you called it, but rather less densely populated. I can easily see R1a and R1b arising somewhere in or near Kazakhstan, either in the east (Altai area) or west (Ural-Volga region). The western Kazakhstan area (Ural-Volga) could easily have been continuously populated during the LGM. and it isn't all that far from the Caucasus. So I think it is quite possible.
------------Ken
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Hi KM
Yes it is a big area; but it was a big empty area between 22-16000 BC. I don't have the time to look up and list an extensive reference base, but you can see "The Eastern Gravettian “Kostenki Culture” as an Arctic adaptation" by John hoffecker (which shows that Russian plain was depopulated) and "Modern Human Colonization of the Siberian Mammoth Steppe: A View from South-Central Siberia" by Graf (where she bunks older arguements that Siberia was continuously populated during the LGM) . Also note that mal'ta was the "last of his kind" in Siberia ; although the met-population from which he derived survived to later contribute to EHG and Americans . So where was this refuge ? Possibly the Altai ; where there is a continuous typology of micro blade development (but no human or settlement evidence); or possibly anywhere in southern Central Asia which was warmer but modern research is still at a poor stage

I have no personal investment as to where r1b as a whole originated from, but the above settlement evidence combined with modern phylogeny of two branches parallels (V88, M343) to M297 suggestive of an epicentre somewhere south of the Caucasus makes the idea of M343 originating in the steppe non-parsimonious, but certainly not impossible given the caution we must exercise when analysing through the veil of modern patterns , and what we know about the dynamic character of human settlement / demography in general

alan
10-23-2015, 04:17 PM
Sorry but the paper by Graf does NOT debunk older arguments that Siberia was continuously populated during the LGM. The population was low, as one would expect. Graf says: "At about 24,000 cal BP, populations in southcentral Siberia dwindled to archaeologically unrecognizable levels. Whether or not humans completely disappeared from Siberia during the LGM is not known; however, in the Enisei River basin populations seemed to have been quite low."

This does not sound like a "big empty area" as you called it, but rather less densely populated. I can easily see R1a and R1b arising somewhere in or near Kazakhstan, either in the east (Altai area) or west (Ural-Volga region). The western Kazakhstan area (Ural-Volga) could easily have been continuously populated during the LGM. and it isn't all that far from the Caucasus. So I think it is quite possible.
------------Ken
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Graf says: "At about 24,000 cal BP, populations in southcentral Siberia dwindled to archaeologically unrecognizable levels. Whether or not humans completely disappeared from Siberia during the LGM is not known; however, in the Enisei River basin populations seemed to have been quite low."

Actually the reality is that apart from Mal'ta boy at 22000BC there are not any radiocarbon dates for settletment in south central Siberia (which had previously be occupied) after 24/25000BC and through the LGM. I have always had the suspicion that Mal'ta boys date is not correct because he dates 2-3000 years later than anyone else in his culture (rest of dates are 30000-25000BC) or the region he was living in - which was 2-3000 years into the LGM which makes it even more suspect. I wouldnt be surprised if his real date was 25/24000BC. Something worth bearing in mind when discussing SNP counting based on Mal'ta.

The only known LGM refuge within the territory of the middle upper palaeolithic culture Mal'ta boy was a very late member of 30000-22000BC is Altai. However the actual techniques of Mal'ta boy's cultures ended around the time he lived and the incipient use of microblades fully bloomed instead through the LGM. Expansion back into the areas to the north was a post-LGM thing associated with microblades.

Krefter
11-14-2015, 03:46 PM
String of R1b M269(xL23) in Balkans, Italy, and West Asia. There are also scattered occurrences. R1a(xM17) in Turkey, Iran, Italy, and Germany. R1b(xM269, M73, V88) in Germany, Slovakia, Ukraine, Tatar, Romania, Kurds, and Turkey.

Supp. information Table S$ Myers 2010. (http://www.nature.com/ejhg/journal/v19/n1/suppinfo/ejhg2010146s1.html)

Tomenable
12-01-2015, 11:35 AM
"The R1b1 and R1a1 from Mesolithic Russia are dead-lineages. IMO, there's a high possibility both M417 and L23 are from West Asia."

The Karelian guy is only ancestral to M417.

The Karelian guy lived 7000-7500 years ago and he was xM198, while M198 emerged 14300 years ago (per YFull).

So he was not ancestral to M198 (and by extension not to M417), but he was a "cousin" lineage.

Kale
12-06-2015, 07:41 PM
You have to figure with the massive back and forth turnovers in the bronze age, as evidenced by the overwhelming majority of R1a and to a lesser extent R1b being represented by just a few clades of shallow coalescence, many areas with basal lineages are likely not the epicenter, but the outskirts...the places that got ran over the least.

glentane
12-06-2015, 08:19 PM
One of the mental hurdles I constantly have to hop is that "outskirts" all depend on the modes of transport available at any one time. For instance, horses are a no no in the Northern Forest even in summer (no fodder), and need tying up and shoving into substantial boats to get to islands. But they're just the job for racketing around Central Europe etc.

Places which seem remote today *Orkney cough cough* were pretty much rest-stops for ship-using Continental or Isles marauders going north or south, from the local Bronze Age until Mediaeval times, and were always in danger of extermination and replacement. The MacDonalds of Eigg, for instance, were wiped out by their MacLeod neighbours in a seemingly interminable clan war (http://www.walkhighlands.co.uk/skye/clans.shtml) which petered out by the 17th century, possibly for lack of participants on both sides.

Theramster
08-09-2016, 09:15 PM
I think the biggest holes in the data are North Central Asia and South Asia. There is all kinds of crazy stuff in North Central Asia but because of the tendency to tribal founder effects sampling one or two populations will get you a whole lot of one common haplogroup and not much of the rarer stuff. Like with Kazakhs, where one study finds they are massively G1, another they are mostly R1a, another they'll be mainly C2b. The same thing happens in South Asia because the groups are endogamous, and there are over a billion inhabitants, it is ludicrously undersampled.

Most studies are not resolved below M269, so it is hard to tell whether it is L23 or not. For M269(xL23) the only unusual element of distribution I can think of is that it is present in North Africa at higher level than in most of Europe or West Asia (3/297 according to Bekada).

Since you have all the West Eurasian data I do, here is South and East Asia:

Tibet: 4/2354 R1b-M343(xM335, M73, M269), I'd guess R1b-PH1165; also 2/2354 R1b-M73; no M269 at all; 1/2354 R1*(xR1b-M343, R1a1a-M17) - could be basal R1a.
Ladakh (Kashmir region): 1/215 R1b-M335; 1/215 R1a1*-SRY1532(xR1a1a-M17).
India: 2/1152 R1a1*-SRY1532(xR1a1a-M17) (1 upper caste North Indian, 1 Munda tribal); 13/1152 R1*-M173(xR1a1-SRY1532, R1b1a2-M269) - mostly in low-middle caste Dravidian speakers from South India. (Trivedi 2007, pretty old and maybe not that reliable).
Bali: 2/641 R1b1-P25(xM269) - Bali has a lot of Indian Y DNA so could be from there
Southern China: 1/447 Yunnanese had R1b-M335 (Hua Zhong et al 2011);
Northern China: 3/853 Northern Han R1b-M73 (all from Gansu, which is quite far in the northwest); 1/853 R1b*-M343 (xM269, M73, M335) - from Shandong, in the east.

There is very, very little properly tested data from South Asia.

No frequency data available, but R1b-PH1165, the most basal form, is reported in a Tajik and a Bhutanese, and from private testing probably also in 2 Indians and a Uyghur from Xinjiang.
Do you happen to have the STR values of these data? I'd appreciate if you provided a link. Thank you.

Megalophias
08-09-2016, 09:30 PM
Do you happen to have the STR values of these data? I'd appreciate if you provided a link. Thank you.
I don't, but see the post below that one with links to the studies, some of them probably have STR data.

Theramster
08-16-2016, 07:28 PM
Yes you're right karelian sample is not ancestral to R1a1a (R-M198 and all subclades). Any STR data from the karelian sample?

Theramster
08-16-2016, 07:29 PM
The Karelian guy lived 7000-7500 years ago and he was xM198, while M198 emerged 14300 years ago (per YFull).

So he was not ancestral to M198 (and by extension not to M417), but he was a "cousin" lineage.

Yes you're right karelian sample is not ancestral to R1a1a (R-M198 and all subclades). Any STR data from the karelian sample?