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alan
07-30-2013, 11:08 AM
I think if the current clade dates were considered spot on then it would have implications that have not been fully worked through. I want this conversation on the basis that R1a and b were not in farming areas before 5000BC which I think is pretty clear from the branching or lack of it before then and indeed for some time after. So essentially the scope of this thread based on a steppe or near-steppe model where their expansion only commences at the end of the Neolithic and early copper age of the region. If you dont agree with the model then that is fair enough but this thread is based on a temporary assumption that this is correct.

So, in terms of R1a and R1b clades we need to consider the ages and on that basis what cultures or waves they could have been involved in.

To kick off, the first steppe wave into the Lower Danube and adjacent which Anthony associates with Anatolian and sees these peoples as having moved from the Dneiper to the Danube/Balkans and then onto Anatolia later. This is dated to 4200BC initially. Are there any R1a and b clades actually old enough? It seems to me there should be some sort of trail through of a clade of an old enough age in the Balkans and Anatolia although the steppes themselves are probably a lost cause in terms of a modern trail.

In terms of R1b the only clade that appears to be potentially old enough and with a distribution that might have some slighly displaced correlation would be M269xL23 which is found in the Balkans, in possibly Balkans-derived Armenians and in Anatolians. I am not saying that existing M269 is old but at least in theory it branched early enough.

L23 is normally dated c. 3500BC somewhat later so either it had to be a later wave or perhaps it could even have occurred in situ among M269 immigrants in the Balkans. Both options have pros and cons.

Is there an R1a clade old enough to correlate with this early wave? Remember that there can easily be paradox as the ultimate area these lineages may have ended up may have been Anatolia with perhaps traces in the Balkans so there is no problem if it has a non-steppe distribution today given its complex history.

alan
07-30-2013, 04:10 PM
In terms of the other direction, what about the Afanasievo-Tocharian link. By that sort of period 3500BC M73 had had 1500 years to grow and could have been a substantial player somewhere. very few of the other R1b or R1a clades had had any sort of time to grew by 3500BC if the suggested variance dates are correct. How long had the relevant R1a clades been in existence around the time the Tocharians headed east? According to the dated R1a tree posted on another thread, the Z94 group did not exist at the point of the Afansievo culture and the Z93 group would have just been one man in 3500BC. So, you could argue M73 is the only R1b or R1a clade on the steppes today old enough to have been involved in Afanasievo.

alan
07-30-2013, 04:34 PM
It can also be argued that other than the odd NW European group almost all of the European group split from one guy who on the R1a chart is placed as living about 3300BC. An excellent fit for Yamnaya but leaves very little evidence that R1a was involved in the pre-Yamnaya waves west from 4200-3300BC which are discussed at some length by Anthony.

Now I have already commented on r1a clades appearing to be somewhat too young to be involved in Afanasievo.

R1b's major branches M73 around 5000BC and M269 most commonly placed around 4-5000BC are old enough to have taken place in pre-Yamnaya movements such as Suvorovo and others west and Afanasievo east. Even L23 is usually dated to 3500BC, again somewhat older than the common ancestors of the main European and Asian groups. So, perhaps the old theory of an earlier R1b migration out of the steppe west and east followed by R1a Yamnaya groups does have a basis. Is the difference in R1a and R1b partly to do with chronology then. R1b has always had a peculiar pattern in eastern Europe suggestive of it being a patchy substrate and if it was largely an early wave that was subsequenly replaced etc that would not be a surprise at all.

newtoboard
07-30-2013, 05:47 PM
In terms of the other direction, what about the Afanasievo-Tocharian link. By that sort of period 3500BC M73 had had 1500 years to grow and could have been a substantial player somewhere. very few of the other R1b or R1a clades had had any sort of time to grew by 3500BC if the suggested variance dates are correct. How long had the relevant R1a clades been in existence around the time the Tocharians headed east? According to the dated R1a tree posted on another thread, the Z94 group did not exist at the point of the Afansievo culture and the Z93 group would have just been one man in 3500BC. So, you could argue M73 is the only R1b or R1a clade on the steppes today old enough to have been involved in Afanasievo.

That is highly speculative based on dates that might not be accurate. It also isn't ridiculous to say that they might have been Z93*, Z283* or anything upstream of that.

alan
07-30-2013, 09:57 PM
That is highly speculative based on dates that might not be accurate. It also isn't ridiculous to say that they might have been Z93*, Z283* or anything upstream of that.

Even those two clades would be around 3500BC and would be one man. It is entirely possible that the real dates are out or not at the centre of the confidence interval are out as you say although that in itself is worth bringing up if it does lead to problems correlating with archaeological dating. However, they should be at least relatively right and it does stand that R1b clades like M269, L23 and M73 in the right general longitude do seem older than the R1a clades. That probably is providing us with some nuance about the differences in their stories.

I would still say that the main R1a clades of eastern and central Europe and Asia do fit the traditional Yamnaya origin rather well as well as somehow also being involved in the genesis of Corded Ware. However, the earliest steppe waves west into the Balkans, which started perhaps 4200BC seem nearly 1000 years too early for the branching root of those clades, which itself is often significantly older than coalecense/intraclade dates. It just seems to me that R1b has a couple of clades that are significantly older in terms of interclade variance than R1a ones. So, although we often discuss origin point and directions of expansions the differences in modern distribution may also owe a significant amount to chronological differences in the first periods of early expansion.

It is also striking that the R1b does strongly tend to be associated with the earlier branching off the IE tree - I think Tocharian is best put aside for now as there is too much uncertainty about it. I think there are hints in the DNA branching that the chronological differences may be as big a factor as initial location. The step waves are also divided into the early period 4200BC-3500BC and the big Yamnya phase which seems to have largely entered Old Europe after 3000BC according to Heyd's recent paper. So, there could be a sequence in a steppe model that would explain the differences.

I think the actual clade pattern of the European steppes itself in 4500-3000BC has been close to erased today. However, it is possible to guess that there could have been a sequence that led to the present associations of R1 with various languages. It makes a certain amount of sense to see R1b as associated with the early exit from the steppes and R1a as following this up in the Yamnaya period. This is of course contrary to my Maykop speculations. However I have an open mind on this and it would also make a lot of sense if R1b was associated with the earlier waves from the steppe before 3500BC. The westerly steppe groups close to the farming boundary in the period 4500BC included the Sredny Stog, Skerla type groups. They appear to have also been mixed groups judging by craniology although probably with a tendency to revert back towards the steppe type due to weight of numbers and female marriage pool. Other groups near the farming boundary were apparently similarly mixed including Mikhailovka I who stretched from the Crimea, Dneiper to the Danube mouth along the Black Sea. These groups simply must have been mixed in terms of yDNA and I would suspect they included non-R lines from the farming world like J2.

It is possible that R1b could have entered the steppe with farmers when they became part of these mixed groups but I suspect R1b already had a place on the western steppes. I say this because M269 only dates from 4000BC or a little earlier and there are simply no traces of its P297* ancestors of the previous 5000 years, not something you would expect in the farming world and certainly not some enormously expanding group like Cuc-Trp. However, it is possible to picture this in the steppe world.

Regardless, I am not bothered about whether R1b was indigenous to the western steppes hunters or intrusive. Its not really important. The main point is there were clearly mixed groups in the western part of the European steppes c 4500-3500BC, further mixed by Maykop elements towards the end of that period, and they all would have been on-scene when PIE proper evolved and were therefore part of the PIE population.

So, puttinh on a pure steppes model hat, I would think that R1b may have been within Stredy Stog groups in the Dnieper-Don area and part of the Skerla-Novodanilkova-Suvorovo elite who were already well linked to the farming world to the west from c. 4500BC before they infiltrated from 4200BC and for some time after. If I had to guess I would suggest they were a predominantly R1b-and non-R mixture. In a purely steppe model I would think R1a was contained in the Late Khvalynsk-Repin groups further east who seem most ancestral to Yamnaya and underwent its main expansion from there with that culture. I actually have a funny feeling M73 got early mixed into this group and somewhat separated from M269.

leonardo
07-30-2013, 10:48 PM
http://www.familytreedna.com/public/R1a/

Michał
07-31-2013, 03:50 PM
To kick off, the first steppe wave into the Lower Danube and adjacent which Anthony associates with Anatolian and sees these peoples as having moved from the Dneiper to the Danube/Balkans and then onto Anatolia later. This is dated to 4200BC initially. Are there any R1a and b clades actually old enough?

I agree with newtoboard that the methods used for dating some relatively old R1a or R1b subclades are not accurate enough to determine with high probability whether a given branch expanded let’s say 4200 or 3600 BC. The margin of error is usually too large in all such cases.

When regarding your above question, the R1a-Z645 branch seems to be old enough. Even the expansion of each of its two major sub-branches, i.e. Z93 and Z283, could be potentially dated to the 4200-3600 BC period. However, both these clades seem to be strongly associated with some very specific branches of IE (Indo-Iranian and Balto-Slavic, respectively), hence it seems nearly impossible that any of them could have been also specifically associated with the very early separated Anatolian branch. Also, no Z645* cases have been found that could have potentially correspond to the Anatolian branch. Thus, associating R1a with Anatolians seems to be indeed a very risky move.

Let me also make some comments regarding the suggested association between the Suvorovo-Novodanilovka group and the Pre-Anatolians. There are actually many reasons why I think this connection is rather unlikely:

1) The linguistic distance between the Anatolian, Tocharian and Late PIE branches is IMO much too large to correspond to the very small time periods between 4000 BC (when the Suvorovo group could have been separated from the remaining Sredny Stog/Khvalynsk group), 3300 BC (or actually any date between 4000 and 3000 BC suggested for the separation of the Tocharian branch) and 3000 BC (when the Corded-Ware-related Balto-Slavic branch is supposed to have been separated from the rest). Actually, the difference between the Anatolian and all remaining IE languages is so huge, that I doubt it can be explained by any strong influence of the local substratum met in Anatolia. IMO, this rather suggests some very early separation of the Anatolian branch, followed by at least 1500 years until the Tocharian-related split took place and at least next 500 years before the Late PIE unity was broken.

2) After Suvorovo-Novodanilovka has contributed to the Cernavoda culture (4000-3200 BC), its further expansion was mostly directed west towards Central Europe, and much less towards Anatolia. Apart from the appearance of the Ezero culture (3300-2700 BC) that is considered to be a “missing link” between the steppe and Anatolia , this has led to the formation of the Baden (3600-2800 BC), Cotofeni (3500-2500 BC) and Vucedol-Kostolac (3000-2000 BC) cultures, suggesting that all these cultures, forming the so-called Balkan-Danubian complex, were created by people speaking an archaic IE language, related to Anatolian. This practically leaves no room for any subsequent “non-Anatolian” Yamna-derived (or Usatovo-derived?) wave of Late PIE-speaking people directed westward. Also, the Yamna-derived Usatovo culture is dated to 3500-3000 BC, which makes the distance between the separation of the Pre-Anatolian-speaking Suvorovo-Cernavoda population and the westward migration of the Late PIE-speaking West Yamna/Usatovo people incredibly small (500-700 years only!). Of course, it seems nearly impossible to place the Tocharian “departure” in between, the way it would make any sense from the linguistic point of view.

3) The PIE-derived wheeled-vehicle vocabulary is actually missing in the Anatolian languages, which makes their connection with Sredny Stog and Suvorovo-Novodanilovka somehow less likely.

4) The only potential Balkan-derived (or steppe-derived) subclade of R1b that could theoretically correspond to the early separated Anatolian branch is the paragroup M269*, and it seems that the age and internal structure of this group is not known well enough to verify the above hypothesis.



So, you could argue M73 is the only R1b or R1a clade on the steppes today old enough to have been involved in Afanasievo.
I cannot agree with that. I’ve seen the R1a-Z93 branch being dated to about 3500 BC, 3700 BC, and most recently to about 4100 BC (in the Igor Rozhanskii’s latest tree), so I see no reason to exclude this R1a clade from a group of potential contributors to Afanasevo. Also, newtoboard is right that in the case of Afanasevo we cannot exclude finding an extinct sister clade (or some early separated subclade) of Z93.




R1b's major branches M73 around 5000BC and M269 most commonly placed around 4-5000BC are old enough to have taken place in pre-Yamnaya movements such as Suvorovo and others west and Afanasievo east. Even L23 is usually dated to 3500BC, again somewhat older than the common ancestors of the main European and Asian groups.
There are several issues that need to be resolved before speculating on any specific involvement of M73, M269*, Z2105 and L51 in the hypothetical IE-related movements in Eurasia.

First, I suspect that the date you provide for M73 is a coalescence age (or TMRCA) for the entire clade, including the potential Western European sub-branch that seems to be very distantly related to the potential Eastern (Eurasian) branch. I would love to compare TMRCAs calculated for the entire M73 clade with those provided for the Western subgroup, Eastern subgroup, and two apparent subgroupings of the Eastern group, respectively.

Secondly, I guess the above-mentioned age for M269 (4-5000 BC) is supposed to represent TMRCA for the entire M269 clade, while when looking for some possible associations between M269* and the Anatolian branch we need to know the age estimation for M269*, i.e. for M269(xL23). Also, it would be extremely useful to know the geographical distribution and age of some evident STR-based clusters within this group. For example, it is crucial to estimate whether the Balkan (and specifically East Balkan) population of the M269* members indeed represents the oldest group or is rather a recently expanded potential subclade that is much younger than the Anatolian, “East Caspian”, or even Italian group. We simply need to know both the structure and the distribution of the M269* paragroup, before trying to correlate it with any prehistoric IE-related population movements.

Thirdly, are there any reliable age estimations for the Z2105 clade (or the L23(xL51) group) and for its major subclades L584 and L277?



However, they should be at least relatively right and it does stand that R1b clades like M269, L23 and M73 in the right general longitude do seem older than the R1a clades.
I think you are exaggerating the difference between the estimated ages for the major subclades of R1a and R1b, respectively. For example, I’ve seen M269 being estimated to be 5.7-7.0 ky old, M73 to be 7.2-8.0 ky old, L23 to be 5.7-7.0 ky old and L51 to be about 4.9 ky old. These TMRCAs are actually at the same level as similar estimations for particular subclades of R1a, including M417 (7.1-7.6 ky), CTS4385 (6.5 ky), Z645 (6.0-6.2 ky), Z93 (5.5-6.1 ky) and Z283 (5.5-5.8 ky).

Jean M
07-31-2013, 04:11 PM
I agree with newtoboard that the methods used for dating some relatively old R1a or R1b subclades are not accurate enough to determine with high probability whether a given branch expanded let’s say 4200 or 3600 BC. The margin of error is usually too large in all such cases.

This is crucial. I couldn't agree more.

alan
08-01-2013, 12:51 AM
Well if nothing else the thread has led to the pointing out of difficulties that would arise in interpretation if the most commonly quoted dates were literally true. I do notice a general feeling feeling that ages may be underestimates cropping up. I must admit I have had a nagging feeling in the same direction for a long time.

jeanL
08-01-2013, 11:42 PM
It looks like STR based age estimates using the currently derived mutations rates produce estimates that are several order of magnitude too young.




We have compared phylogenies and time estimates for Y-chromosomal lineages based on resequencing ∼9 Mb of DNA and applying the program GENETREE to similar analyses based on the more standard approach of genotyping 26 Y-SNPs plus 21 Y-STRs and applying the programs NETWORK and BATWING. We find that deep phylogenetic structure is not adequately reconstructed after Y-SNP plus Y-STR genotyping, and that times estimated using observed Y-STR mutation rates are several-fold too recent. In contrast, an evolutionary mutation rate gives times that are more similar to the resequencing data. In principle, systematic comparisons of this kind can in future studies be used to identify the combinations of Y-SNP and Y-STR markers, and time estimation methodologies, that correspond best to resequencing data.

So not the central variance dates using germline mutation rates cannot be taken at facevalue. I have yet to read the paper, so I won't fully comment on it, but my opinion is that the evolutionary rate produces a rough estimate of the age, but it is far more complicated than that. A far better estimate would be produced if we were to use slow mutating markers and while using a linearization about a given modal value correct for the change in mutation rate as a function of repeat number.

alan
08-02-2013, 12:43 AM
We desperately need a lot more ancient DNA data points to feel more confidence but to date it seems to agree with the estimates. There are enormous gaps though so nothing would surprise me. I do think though that any adjustment across the boards is limited by European haplogroup I already having an old date of c. 25000BC estimate and humans in Europe being no more than about 40000 years old. So I think there is a limit on just how out the dates could be out by i.e at worst they couldnt even be doubled. Adjusting I to the earliest possible date would still only make west European P312 perhaps date to 6000bc which is approximately the early Neolithic. Ancient DNA doesnt support this as yet.


It looks like STR based age estimates using the currently derived mutations rates produce estimates that are several order of magnitude too young.



So not the central variance dates using germline mutation rates cannot be taken at facevalue. I have yet to read the paper, so I won't fully comment on it, but my opinion is that the evolutionary rate produces a rough estimate of the age, but it is far more complicated than that. A far better estimate would be produced if we were to use slow mutating markers and while using a linearization about a given modal value correct for the change in mutation rate as a function of repeat number.

alan
08-02-2013, 12:59 AM
I agree with newtoboard that the methods used for dating some relatively old R1a or R1b subclades are not accurate enough to determine with high probability whether a given branch expanded let’s say 4200 or 3600 BC. The margin of error is usually too large in all such cases.

When regarding your above question, the R1a-Z645 branch seems to be old enough. Even the expansion of each of its two major sub-branches, i.e. Z93 and Z283, could be potentially dated to the 4200-3600 BC period. However, both these clades seem to be strongly associated with some very specific branches of IE (Indo-Iranian and Balto-Slavic, respectively), hence it seems nearly impossible that any of them could have been also specifically associated with the very early separated Anatolian branch. Also, no Z645* cases have been found that could have potentially correspond to the Anatolian branch. Thus, associating R1a with Anatolians seems to be indeed a very risky move.

Let me also make some comments regarding the suggested association between the Suvorovo-Novodanilovka group and the Pre-Anatolians. There are actually many reasons why I think this connection is rather unlikely:

1) The linguistic distance between the Anatolian, Tocharian and Late PIE branches is IMO much too large to correspond to the very small time periods between 4000 BC (when the Suvorovo group could have been separated from the remaining Sredny Stog/Khvalynsk group), 3300 BC (or actually any date between 4000 and 3000 BC suggested for the separation of the Tocharian branch) and 3000 BC (when the Corded-Ware-related Balto-Slavic branch is supposed to have been separated from the rest). Actually, the difference between the Anatolian and all remaining IE languages is so huge, that I doubt it can be explained by any strong influence of the local substratum met in Anatolia. IMO, this rather suggests some very early separation of the Anatolian branch, followed by at least 1500 years until the Tocharian-related split took place and at least next 500 years before the Late PIE unity was broken.

2) After Suvorovo-Novodanilovka has contributed to the Cernavoda culture (4000-3200 BC), its further expansion was mostly directed west towards Central Europe, and much less towards Anatolia. Apart from the appearance of the Ezero culture (3300-2700 BC) that is considered to be a “missing link” between the steppe and Anatolia , this has led to the formation of the Baden (3600-2800 BC), Cotofeni (3500-2500 BC) and Vucedol-Kostolac (3000-2000 BC) cultures, suggesting that all these cultures, forming the so-called Balkan-Danubian complex, were created by people speaking an archaic IE language, related to Anatolian. This practically leaves no room for any subsequent “non-Anatolian” Yamna-derived (or Usatovo-derived?) wave of Late PIE-speaking people directed westward. Also, the Yamna-derived Usatovo culture is dated to 3500-3000 BC, which makes the distance between the separation of the Pre-Anatolian-speaking Suvorovo-Cernavoda population and the westward migration of the Late PIE-speaking West Yamna/Usatovo people incredibly small (500-700 years only!). Of course, it seems nearly impossible to place the Tocharian “departure” in between, the way it would make any sense from the linguistic point of view.

3) The PIE-derived wheeled-vehicle vocabulary is actually missing in the Anatolian languages, which makes their connection with Sredny Stog and Suvorovo-Novodanilovka somehow less likely.

4) The only potential Balkan-derived (or steppe-derived) subclade of R1b that could theoretically correspond to the early separated Anatolian branch is the paragroup M269*, and it seems that the age and internal structure of this group is not known well enough to verify the above hypothesis.



I cannot agree with that. I’ve seen the R1a-Z93 branch being dated to about 3500 BC, 3700 BC, and most recently to about 4100 BC (in the Igor Rozhanskii’s latest tree), so I see no reason to exclude this R1a clade from a group of potential contributors to Afanasevo. Also, newtoboard is right that in the case of Afanasevo we cannot exclude finding an extinct sister clade (or some early separated subclade) of Z93.



There are several issues that need to be resolved before speculating on any specific involvement of M73, M269*, Z2105 and L51 in the hypothetical IE-related movements in Eurasia.

First, I suspect that the date you provide for M73 is a coalescence age (or TMRCA) for the entire clade, including the potential Western European sub-branch that seems to be very distantly related to the potential Eastern (Eurasian) branch. I would love to compare TMRCAs calculated for the entire M73 clade with those provided for the Western subgroup, Eastern subgroup, and two apparent subgroupings of the Eastern group, respectively.

Secondly, I guess the above-mentioned age for M269 (4-5000 BC) is supposed to represent TMRCA for the entire M269 clade, while when looking for some possible associations between M269* and the Anatolian branch we need to know the age estimation for M269*, i.e. for M269(xL23). Also, it would be extremely useful to know the geographical distribution and age of some evident STR-based clusters within this group. For example, it is crucial to estimate whether the Balkan (and specifically East Balkan) population of the M269* members indeed represents the oldest group or is rather a recently expanded potential subclade that is much younger than the Anatolian, “East Caspian”, or even Italian group. We simply need to know both the structure and the distribution of the M269* paragroup, before trying to correlate it with any prehistoric IE-related population movements.

Thirdly, are there any reliable age estimations for the Z2105 clade (or the L23(xL51) group) and for its major subclades L584 and L277?



I think you are exaggerating the difference between the estimated ages for the major subclades of R1a and R1b, respectively. For example, I’ve seen M269 being estimated to be 5.7-7.0 ky old, M73 to be 7.2-8.0 ky old, L23 to be 5.7-7.0 ky old and L51 to be about 4.9 ky old. These TMRCAs are actually at the same level as similar estimations for particular subclades of R1a, including M417 (7.1-7.6 ky), CTS4385 (6.5 ky), Z645 (6.0-6.2 ky), Z93 (5.5-6.1 ky) and Z283 (5.5-5.8 ky).

I have heard dates as early as 4300BC for the earliest steppe groups heading west while on the other hand Heyd does put Yamnaya west of the Black Sea c. 3000BC at the earliest. So there is a pretty large gap in time between them.

On the point of the wheel, the wheel probably first appeared on the steppe fringes around 3500BC so the suvorovo and related early Sredny Stog groups would not have known the wheel at the time of their departure c. 4200BC. Having said that, it is also hard to understand how Anatolians in the Balkans would not have picked up the words aerially if they hung around much after 3500BC because the wheel seems widespread shortly after that.

jeanL
08-02-2013, 02:03 AM
There is this other paper done on Sardinians using Y-DNA SNPs, and calibrating the nodes assuming a settlement of Sardinia based on archaeological data from the initial expansion of the Sardinian population as ~7700 years ago.

Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny (http://www.sciencemag.org/content/341/6145/565.abstract)





Genetic variation within the male-specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1204 Sardinian males identified 11,763 MSY single-nucleotide polymorphisms, 6751 of which have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe, along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal the presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180,000 to 200,000 years ago, which is consistent with previous mitochondrial DNA–based estimates.

See Figure-1:

586

Seems like Basque I-M26 is in fact a different clade from the Sardinian I-M26, and separated before I-M26 experienced its boom.

See Figure-2:

587

Here is what they said about it:




To estimate points of divergence between Sardinian and continental clades, we sequenced two samples from the Basque Country and northern Italy, belonging to haplogroup I, and two, from Tuscany and Corsica, belonging to haplogroup G. We also analyzed the sequence of the so-called Iceman Ötzi (9), together with 133 publicly available European sequences from the 1000 Genomes Project database and those SNPs from the International Society of Genetic Genealogy (ISOGG) database detected outside Sardinia.

The Basque individual separates from the basal position of the I2a1a branch that encompasses 11 Sardinian individuals. The northern Italian sample, instead, most likely reflecting the last step of I2a1 lineages before their arrival in Sardinia, is at the basal point of most of the remaining I2a1a samples (Fig. 2). Considering two other basal lineages encompassing only Sardinian samples, we can infer that when the I2a1a sub-haplogroup entered Sardinia, it had already differentiated into four founder lineages that then accumulated private Sardinian variability. Two other founder clades show similar divergence after entry into the island: one belonging to haplogroup R1b1c (xV35) (whose differentiation is identified contrasting the Sardinian data with the ISOGG and 1000 Genome data), and the other to haplogroup G2a2b-L166 (identified by divergence from a sequenced Corsican sample).

jeanL
08-02-2013, 02:42 AM
What is interesting about this, is that as per Martinez-Cruz.et.al.2012 study of the Basque Country, R1b-P312(xL21,U152,M153,M167) is indeed older in the Basque Country than I-M26, and since it appears that Basque I-M26 did not arrive directly from Sardinia, but rather is an older branch, it makes me wonder about the age of R1b-P312 in Basques. As per Table-2 of the study, they find the age of I-M26 in Basques to be 7.6+-1.8 kya using the evolutionary rate(given the new paper which shows evolutionary estimates to be more in line with Y-SNPs estimates), this date does in fact agree with the Basques I-M26 being basal to Sardinians, and the Sardinian settlement taking place circa 7700 ybp. So at face value that would make Basque I-M26 dated to 5600 BC (R: 3800 BC--7400 BC), by contrast they give the ages of other haplogroups as:

R1b-P312(xL21,U152,M153,M167) as 10.4+-1.8 kya, which would mean that Basque R1b-P312*, likely R1b-DF27 is dated to 8400 BC (R:6600 BC--10200 BC)

R1b-M153 as 6.1+-1.3 kya, this means that R1b-M153 is dated in Basques to 4100 BC (R:2800 BC--5400 BC).

R1b-SRY2627 as 8.4+-1.7 kya, this means that R1b-M167 is dated in Basques to 6400 BC (R:4700 BC--8100 BC)

R1b-L21 as 7.5+-1.7 kya, this means that R1b-L21 is dated in Basques to 5500 BC (R:3800 BC--7200 BC)

alan
08-02-2013, 03:18 AM
What is interesting about this, is that as per Martinez-Cruz.et.al.2012 study of the Basque Country, R1b-P312(xL21,U152,M153,M167) is indeed older in the Basque Country than I-M26, and since it appears that Basque I-M26 did not arrive directly from Sardinia, but rather is an older branch, it makes me wonder about the age of R1b-P312 in Basques. As per Table-2 of the study, they find the age of I-M26 in Basques to be 7.6+-1.8 kya using the evolutionary rate(given the new paper which shows evolutionary estimates to be more in line with Y-SNPs estimates), this date does in fact agree with the Basques I-M26 being basal to Sardinians, and the Sardinian settlement taking place circa 7700 ybp. So at face value that would make Basque I-M26 dated to 5600 BC (R: 3800 BC--7400 BC), by contrast they give the ages of other haplogroups as:

R1b-P312(xL21,U152,M153,M167) as 10.4+-1.8 kya, which would mean that Basque R1b-P312*, likely R1b-DF27 is dated to 8400 BC (R:6600 BC--10200 BC)

R1b-M153 as 6.1+-1.3 kya, this means that R1b-M153 is dated in Basques to 4100 BC (R:2800 BC--5400 BC).

R1b-SRY2627 as 8.4+-1.7 kya, this means that R1b-M167 is dated in Basques to 6400 BC (R:4700 BC--8100 BC)

R1b-L21 as 7.5+-1.7 kya, this means that R1b-L21 is dated in Basques to 5500 BC (R:3800 BC--7200 BC)

As there is no evidence of a Mesolithic intrusion thse dates would point to a Neolithic intrusion. However, there has always been a problem with P312 being linked to the early Neolithic as the parts of Europe with high P312 falls on both sides of the cardial-northern/central European Neolithic divide.

jeanL
08-02-2013, 03:27 AM
As there is no evidence of a Mesolithic intrusion thse dates would point to a Neolithic intrusion. However, there has always been a problem with P312 being linked to the early Neolithic as the parts of Europe with high P312 falls on both sides of the cardial-northern/central European Neolithic divide.

But the age of R1b-P312(xL21,U152,M153,M167) is calculated as 10.4+-1.8 kya, which would mean that Basque R1b-P312*, likely R1b-DF27 is dated to 8400 BC (R:6600 BC--10200 BC).

These is way before the arrival of the Neolithic in the Basque Country, even while using the lowermost bound date of 6600 BC or 8600 ybp.

lgmayka
08-03-2013, 02:29 PM
But the age of R1b-P312(xL21,U152,M153,M167) is calculated as 10.4+-1.8 kya
That number was calculated using the Zhivotovsky fudge factor (http://bhusers.upf.edu/dcomas/wp-content/uploads/2012/03/Martinez-Cruz2012.pdf).

jeanL
08-03-2013, 02:36 PM
That number was calculated using the Zhivotovsky fudge factor (http://bhusers.upf.edu/dcomas/wp-content/uploads/2012/03/Martinez-Cruz2012.pdf).

Yes, I've never said otherwise, but have you seen the new paper published by Wei.et.al.2013 where they find that the so called evolutionary rate provides a better estimate than the germline mutation rates?

lgmayka
08-03-2013, 02:37 PM
There is this other paper done on Sardinians using Y-DNA SNPs, and calibrating the nodes assuming a settlement of Sardinia based on archaeological data from the initial expansion of the Sardinian population as ~7700 years ago.
Why would anyone assume that Sardinians underwent no bottlenecks or introgressions in the past 7700 years?

Dienekes makes the same point (http://dienekes.blogspot.com/2013/08/new-papers-on-human-y-chromosome.html):
---
The Francalacci et al. rate was calibrated by "the initial expansion of the Sardinian population". Now, whether the current Sardinian population is descended from that initial expansion or from a later successful founder remains to be seen. In any case, using their ultra-slow mutation rate...
---

The bottom line is that the new paper gets tangled in the same confusion that Zhivotovsky did, resulting in similar incorrect estimates.

jeanL
08-03-2013, 02:51 PM
Why would anyone assume that Sardinians underwent no bottlenecks or introgressions in the past 7700 years?

Dienekes makes the same point (http://dienekes.blogspot.com/2013/08/new-papers-on-human-y-chromosome.html):
---
The Francalacci et al. rate was calibrated by "the initial expansion of the Sardinian population". Now, whether the current Sardinian population is descended from that initial expansion or from a later successful founder remains to be seen. In any case, using their ultra-slow mutation rate...
---

The bottom line is that the new paper gets tangled in the same confusion that Zhivotovsky did, resulting in similar incorrect estimates.

We are talking about different papers here:

First there is the Wei.et.al.2013 paper which concluded that out of all the STRs methods for estimating TMRCA the evolutionary rate fits best with SNPs mutation data.


We have compared phylogenies and time estimates for Y-chromosomal lineages based on resequencing ∼9 Mb of DNA and applying the program GENETREE to similar analyses based on the more standard approach of genotyping 26 Y-SNPs plus 21 Y-STRs and applying the programs NETWORK and BATWING. We find that deep phylogenetic structure is not adequately reconstructed after Y-SNP plus Y-STR genotyping, and that times estimated using observed Y-STR mutation rates are several-fold too recent. In contrast, an evolutionary mutation rate gives times that are more similar to the resequencing data. In principle, systematic comparisons of this kind can in future studies be used to identify the combinations of Y-SNP and Y-STR markers, and time estimation methodologies, that correspond best to resequencing data.

Then there was the second paper about Sardinians. Which I agree their SNP mutation rate is far too slow, so it is better to use the mutation rate of 0.82 SNP/bp/year than the one they found of 0.53 SNP/bp/year.

alan
08-03-2013, 04:34 PM
But the age of R1b-P312(xL21,U152,M153,M167) is calculated as 10.4+-1.8 kya, which would mean that Basque R1b-P312*, likely R1b-DF27 is dated to 8400 BC (R:6600 BC--10200 BC).

These is way before the arrival of the Neolithic in the Basque Country, even while using the lowermost bound date of 6600 BC or 8600 ybp.

Could be that population displacement or movement is involved and its not safe to look at groups like they have been in situ or that all variance was created in situ. I imagine if people looked at P312 across Europe they would find similar or older variance for P312 clades. Seems from previous work that higher variance exists around the Alps. So, that creates an issue of how P312 would have spread around in a timeframe of 6600 BC--10200 BC. There is no out of SW Europe movement as late as that. The Magdallenian movements were done and spread all across Europe by even the earliest date in that range. I am not aware of pre-Neolithic movements into Iberia in that timeframe. So I dont think even based on these dates that pre-farming sense can be made of P312 clades. Some sort of link to farming cultures moving west seems more likely to me if those date ranges were to be believed. In a farmer model its likely that a number of founders would have moved so that would effect variance too. I am a little suspecious anyway that the P312 group could be getting distorted by at least a little non-DF27. I would like to see what dates are arrived at for U152 for example. Its usually thought at least as old as DF27.

jeanL
08-03-2013, 07:28 PM
Could be that population displacement or movement is involved and its not safe to look at groups like they have been in situ or that all variance was created in situ. I imagine if people looked at P312 across Europe they would find similar or older variance for P312 clades.[…]So, that creates an issue of how P312 would have spread around in a timeframe of 6600 BC--10200 BC. There is no out of SW Europe movement as late as that. The Magdallenian movements were done and spread all across Europe by even the earliest date in that range. I am not aware of pre-Neolithic movements into Iberia in that timeframe.

Well these calculations only apply to R1b-P312(xU152,L21,M153,M167) found in the Basque Country. Other areas of Europe will display different variance, and different haplogroups. What it is clear is that amongst Basques R1b-P312(xU152,L21,M153,M167) is the oldest haplogroup, so it was the first to arrive, or the oldest one to survive to present day, whichever way you want to put it. What sort of evidence do we have to argue against any movement into the Pyrenean region during the Azilian period from Southern France?


Seems from previous work that higher variance exists around the Alps.

I believe you are referring to the dating put forth my Myres.et.al.2011, if I recall correctly doesn’t that failed to include any trans-Pyrenean populations such as Basques. In any case, if I recall correctly the variance of R1b-DF27 is highest in Iberia, and R1b-DF27 is indeed older than its two siblings.


So I dont think even based on these dates that pre-farming sense can be made of P312 clades. Some sort of link to farming cultures moving west seems more likely to me if those date ranges were to be believed. In a farmer model its likely that a number of founders would have moved so that would effect variance too. I am a little suspecious anyway that the P312 group could be getting distorted by at least a little non-DF27. I would like to see what dates are arrived at for U152 for example. Its usually thought at least as old as DF27.

Unfortunately they didn’t do the dating for R1b-U152, otherwise I would more than gladly post it here. At this point I believe that quoting what you said before sums my feeling right about right:


We desperately need a lot more ancient DNA data points to feel more confidence but to date it seems to agree with the estimates. There are enormous gaps though so nothing would surprise me.

jeanL
08-03-2013, 09:19 PM
Here are some dating of R1b/R1a clades based upon the work of Francalacci.et.al.2013 and Poznik.et.al.2013

If we use the mutation rate calibrated in this paper of 0.53*10-9mut/bp/year we arrive to an average of 205+-50 years per SNP mutation. If instead we use the mutation rate of the Poznik.et.al.2013 of 0.82*10-9mut/bp/year we arrive to an average of 133+-32 years per SNP mutations.

Haplogroup-------------Francalacci.et.al_rate_Age------------------------Poznik.et.al_rate_Age

R1a1a1----------------------------2829 ybp +- 690 ybp----------------------------------1835 ybp +- 442 ybp

R1b1a2*----------------------------7626 ybp +- 1860 ybp --------------------------------4947 ybp +- 1190 ybp

R1b1c*---------------------------15518.5 ybp +- 3785 ybp-------------------------------10068 ybp +-2422 ybp

R2a1------------------------------1743 ybp +- 425 ybp ----------------------------------1131 ybp +- 272 ybp

R1b1a2_Alpha----------------------4715 ybp +- 1150 ybp---------------------------------3059 ybp +- 736 ybp

R1b1a2_Beta-----------------------6027 ybp +- 1470 ybp ---------------------------------3910 ybp +- 941 ybp

Notice that most of R1b1a2(n=185, frequency 15.42%) is made up of R1b1a2_Alpha(n=9, frequency 0.75%), and R1b1a2_Beta(n=175, frequency 14.58%), so there is only 1 R1b1a2 that isn't either R1b1a2_Alpha, or R1b1a2_Beta. Now anyone wants to take a guess as to which clade R1b1a2_Alpha, and R1b1a2_Beta are?


For more ages see here: http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=10786&viewfull=1#post10786

Michał
08-04-2013, 12:50 PM
Notice that most of R1b1a2(n=185, frequency 15.42%) is made up of R1b1a2_Alpha(n=9, frequency 0.75%), and R1b1a2_Beta(n=175, frequency 14.58%), so there is only 1 R1b1a2 that isn't either R1b1a2_Alpha, or R1b1a2_Beta. Now anyone wants to take a guess as to which clade R1b1a2_Alpha, and R1b1a2_Beta are?


The "Alpha" group includes only R1b-M269* people. There should be actually 10 of them, and they all are supposed to share at least nine downstream SNPs (all absent in L23!), so I don't know why one of them has been excluded from this new potential subclade of M269 (i.e. your alpha group). This novel sister clade of L23 is nicely divided into two subclades (with 6 and 4 people, respectively)

The "Beta" group (175 people) is all L23+, and this includes 9 cases of L23* (including three likely cases of L51*, as they all share four downstream SNPs with L11) and 166 cases of L11+. The L11 subgroup includes 3 cases of L11(xP312,Z381), but please note that U106 was not detected (not analysed?). The Z381 group includes two people, including one Z9+. The largest group is of course P312 (161 people) and this includes 128 members of U152, 2 members of L21, 2 members of Z195 and 2 members of Z209 (not recognized as members of Z195!).




R1a1a1----------------------------2829 ybp +- 690 ybp----------------------------------1835 ybp +- 442 ybp

The R1a1a1 group includes 15 people, all belonging to M417. Most of them are Z283+ (11 people), while the remaining four people are Z93+, including one Z93* and three surprising cases of Z2123 (!).

The Z283 group is entirely "Balto-Slavic" and includes 6 putative members of M458, including only one who is CTS11962+ (he is also L1029+), though since CTS11962 is mentioned as a singleton, it is more than likely that its absence in other M458 members is a result of some bad quality readings. L260 has not been found (analysed?).

The remaining 5 cases of Z283 are all Z280+, including one Z280* and four CTS1211+/CTS3607+ people. The CTS3402 mutation has not been found (analysed?), but I suspect that three out of four CTS1211 cases are CTS3402+.

Generally, it is very disappointing that so many SNPs are missed in that analysis (including M417, M458 and Z280, as its presence can only be deduced from the information about some downstream markers). No wonder then that the above age estimates are so incredibly low for this group of R1a (representing both major sub-branches of Z645). The STR-based estimations suggest about 6000-6500 ybp for Z645, while the above SNP-based estimations do not even come close to this number.

As I wrote in another post, when having so many bad quality readings (as in this case), it is almost impossible to use such data to any age estimations, especially if small samples representing a given haplogroup/clade are tested.

R.Rocca
08-04-2013, 01:14 PM
But the age of R1b-P312(xL21,U152,M153,M167) is calculated as 10.4+-1.8 kya, which would mean that Basque R1b-P312*, likely R1b-DF27 is dated to 8400 BC (R:6600 BC--10200 BC).

These is way before the arrival of the Neolithic in the Basque Country, even while using the lowermost bound date of 6600 BC or 8600 ybp.

If most Basque P312* is DF27, then removing M153 and M167 would give an incorrect answer as both are downstream of DF27 and would artificially make the age older than it should be.

alan
08-04-2013, 01:25 PM
I am a little confused about this. Are the calculations saying M269xL23 is younger than L23XL51? How is that possible if its based on SNP counting for that to happen?

Michał
08-04-2013, 01:47 PM
I am a little confused about this. Are the calculations saying M269xL23 is younger than L23XL51?
We don't know this because we haven't estimated the age for L23(xL51), and I am not sure if L51 was analysed in this study. However, this new Sardinian subclade of M269 is definitely younger than its sister clade L23. It would be of course crucial to investigate whether the Balkan, Anatolian and Iranian (or East Caspian) cases of M269* are more closely related to L23 than to this new Sardinian sister clade of L23 (or maybe they rather represent some much more distantly related subclades of M269). This should be actually relatively easy to predict based on some STR data.


How is that possible if its based on SNP counting for that to happen?
It is perfectly possible if estimating the age of the clade as the time to the most recent common ancestor. There are simply at least two subclades of M269, namely L23 and this new Sardinian clade, and either of them can be potentially younger than the other one. I have already asked this question in another thread but let me repeat it once more. Are there any reliable STR-based estimations that would suggest that the M269(xL23) (para)group is older than clade L23 (and if so, into how many potential subclades is this group divided)?

BTW, both Sardinian cases of L21 are DF1+.

jeanL
08-04-2013, 04:18 PM
If most Basque P312* is DF27, then removing M153 and M167 would give an incorrect answer as both are downstream of DF27 and would artificially make the age older than it should be.

Well, I said that most Basque P312* is likely DF27, I don't know if it is, in fact, there is sure to be part of that R1b-P312(xL21,U152,M153,M1670 that is in fact R1b-M65. In any case they dated both R1b-M153, and R1b-M167 to 6.1+-1.3 kya and 8.4+-1.7 kya respectively, so whatever the combined age is, it will likely be in between. They dated everything downstream of R1b-M269+ to 10.7+-2.4 kya, so that would include everything.

R.Rocca
08-04-2013, 05:09 PM
Well, I said that most Basque P312* is likely DF27, I don't know if it is, in fact, there is sure to be part of that R1b-P312(xL21,U152,M153,M1670 that is in fact R1b-M65. In any case they dated both R1b-M153, and R1b-M167 to 6.1+-1.3 kya and 8.4+-1.7 kya respectively, so whatever the combined age is, it will likely be in between. They dated everything downstream of R1b-M269+ to 10.7+-2.4 kya, so that would include everything.

I was just stating the obvious - that their P312* is in fact inflated due to their lack of what we know today - that almost all Iberian P312* (~97%) is in fact DF27 and that M153 and M167 are below DF27. Just shows the dangers of these high level estimates.

alan
08-04-2013, 05:18 PM
We don't know this because we haven't estimated the age for L23(xL51), and I am not sure if L51 was analysed in this study. However, this new Sardinian subclade of M269 is definitely younger than its sister clade L23. It would be of course crucial to investigate whether the Balkan, Anatolian and Iranian (or East Caspian) cases of M269* are more closely related to L23 than to this new Sardinian sister clade of L23 (or maybe they rather represent some much more distantly related subclades of M269). This should be actually relatively easy to predict based on some STR data.


It is perfectly possible if estimating the age of the clade as the time to the most recent common ancestor. There are simply at least two subclades of M269, namely L23 and this new Sardinian clade, and either of them can be potentially younger than the other one. I have already asked this question in another thread but let me repeat it once more. Are there any reliable STR-based estimations that would suggest that the M269(xL23) (para)group is older than clade L23 (and if so, into how many potential subclades is this group divided)?

BTW, both Sardinian cases of L21 are DF1+.

Oh i thought with SNP counting that any clade called M269* had the M269 SNP as its most upstream defining SNP and therefore would have to have SNPs adding up to the time of M269 to today. I didnt realise that date was based on convergence.

jeanL
08-04-2013, 07:25 PM
It seems that if we used the mutation rate Michal mentioned here: http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=10824&viewfull=1#post10824 of 0.7x10-9 mutations/nucleotide/year (CI: 0.6-0.8) which translate roughly into 155 years/mutation +-23 years/mutation. we get some interesting dating for the R1b-L23* date in Sardinians, which is mostly made up of P312+ people(161/175 or 92%), and also U152+ people(128/175 or ~73%).

Sardinian R1b-L23(92% R1b-P312+, 73% R1b-U152+) Age:4557 ybp +-676 ybp

Then we have the Wei.et.al.2012 paper (http://genome.cshlp.org/content/early/2012/10/04/gr.143198.112.abstract) which using a mutation rate of 1x10-9 per bp per year got the following age for R1b(n=13) using rho-2 estimates(which are the ones that use the highest number of bp):

592

But as Dienekes (http://dienekes.blogspot.com/2012/10/calibrated-human-y-chromosome-phylogeny.html) points out, these R1b haplogroups are in fact R1b1a2a1a1b or R1b-P312. If we apply the mutation correction from 1x10-9 to 0.7x10-9, and correcting for the different amount of bp used in the rho-2 estimates namely (8829017 bp) we obtain that using the lower mutation rate we expect 1 mutation per 162 years +-24 years. With this correction we obtain the following age for R1b-P312:

R1b-P312(n=13) Age: 6436 ybp +-953 ybp.

This is interesting as last month rootsweb user Terry Drobb made some TMRCA calculations based on Complete Genomics data, and while calibrating for a CT split of 70 kya arrived to the following age for R1b-P312:


4) Haplogroup R1b-P312 (a subgroup of R1b-M269 found mainly in Western
Europe), would split at 6.1 (+/- 0.6 SD) thousand years ago.

http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2013-07/1372745044

So SNP estimates thus far appear to put the central age of R1b-P312 to ~4200 BC, with the Sardinian age being younger at 2500 BC. This is actually older than the estimates made using STRs.

alan
08-04-2013, 07:54 PM
It seems that if we used the mutation rate Michal mentioned here: http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=10824&viewfull=1#post10824 of 0.7x10-9 mutations/nucleotide/year (CI: 0.6-0.8) which translate roughly into 155 years/mutation +-23 years/mutation. we get some interesting dating for the R1b-L23* date in Sardinians, which is mostly made up of P312+ people(161/175 or 92%), and also U152+ people(128/175 or ~73%).

Sardinian R1b-L23(92% R1b-P312+, 73% R1b-U152+) Age:4557 ybp +-676 ybp

Then we have the Wei.et.al.2012 paper (http://genome.cshlp.org/content/early/2012/10/04/gr.143198.112.abstract) which using a mutation rate of 1x10-9 per bp per year got the following age for R1b(n=13) using rho-2 estimates(which are the ones that use the highest number of bp):

592

But as Dienekes (http://dienekes.blogspot.com/2012/10/calibrated-human-y-chromosome-phylogeny.html) points out, these R1b haplogroups are in fact R1b1a2a1a1b or R1b-P312. If we apply the mutation correction from 1x10-9 to 0.7x10-9, and correcting for the different amount of bp used in the rho-2 estimates namely (8829017 bp) we obtain that using the lower mutation rate we expect 1 mutation per 162 years +-24 years. With this correction we obtain the following age for R1b-P312:

R1b-P312(n=13) Age: 6436 ybp +-953 ybp.

This is interesting as last month rootsweb user Terry Drobb made some TMRCA calculations based on Complete Genomics data, and while calibrating for a CT split of 70 kya arrived to the following age for R1b-P312:



http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2013-07/1372745044

So SNP estimates thus far appear to put the central age of R1b-P312 to ~4200 BC, with the Sardinian age being younger at 2500 BC. This is actually older than the estimates made using STRs.

It would place it in what was the middle Neoltithic of central and southern Europe and the early Neolithic of northern Europe as well as other areas upland and plateau areas not settled before that. It has to be recalled that the early Neolithic LBK and Cardial people of central and southern Europe were choosey about what land they settled and, while they did stretch from the Balkans to the Atlantic or nearby, they actually left the vast majority of the land unsettled both in between the settlement bands of those two cultures and of course the whole area to the north of LBK. That means there was a huge amount of land for Neolithic groups after 5500 or 5000BC to exploit. That sort of period probably saw the start of the spread of cultures contrated on dairy pastoralism judging by lipid traces on pots and apparenty the spread of the genes responsible for the ability of adults to use milk without lots of processing. This period, the middle Neolithic in broad central and southern European terminology is very interesting. The cultures that arose in that period do seem to have owed something to LBK etc but they were post-LBK in age and they clearly were more than just a continuation. It has always seemed a decent possible alternative period to see the spread of R1b across Europe but up to now the variance dates have seemed too young. The recent discussions do allow for the possibility of seeing something like L11 or L51 breaking off and splitting into clades across Europe. It an alternative that we cannot rule out yet IMO until their is agreement on yDNA dating and there is just not enough ancient DNA from that sort of 5000-4000BC period to feel sure we would have picked up what might have still then just been a minority element.

Michał
08-04-2013, 09:07 PM
we get some interesting dating for the R1b-L23* date in Sardinians, which is mostly made up of P312+ people(161/175 or 92%), and also U152+ people(128/175 or ~73%).
[...]
So SNP estimates thus far appear to put the central age of R1b-P312 to ~4200 BC, with the Sardinian age being younger at 2500 BC. This is actually older than the estimates made using STRs.
I think you are forgetting that in contrast to most STR-based age estimations, the SNP-based calculations are (or rather should be) insensitive to some differences in a subclade composition of a given sample (as long as both lineages descending from a given branching point are represented, of course). In other words, it shouldn’t matter whether the Sardinian R1b-L23 sample contains 99% of U152 and 1% of Z2105 or whether the proportions are 50-50 or 1-99. The calculated age of clade L23 (or the Z2105/L51 branching point) should be exactly the same in each case (although there seem to be some “minor” technical limitations that make it much less obvious in practice).

jeanL
08-04-2013, 09:32 PM
Yes, indeed as I said the age for the Sardinian clades is that of R1b-L23, I just mentioned that it was mostly made up of P312 and U152. What do you think of the age of R1b-P312 that I recalculated from Wei.et.al.2012

R1b-P312(n=13) Age: 6436 ybp +-953 ybp.

And the age that Terry Drobb calculated while calibrating for a CT split of 70 kya arrived to the following age for R1b-P312:


4) Haplogroup R1b-P312 (a subgroup of R1b-M269 found mainly in Western
Europe), would split at 6.1 (+/- 0.6 SD) thousand years ago.

http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2013-07/1372745044

alan
08-04-2013, 11:41 PM
I must admit it would be a lot more comfortable archaeologically to have those sort of dates as it at least very broadly would fit into the middle Neolithic infilling of the large amount of unsettled areas in Europe as well as adding to areas already settled. I have posted before years ago that there is a kind of correlation in a lot of Europe with high R1b levels with areas not settled until 5000-3500BC by farmers. You can see this in terms of the whole of northern Europe, the Alpine band as well as areas like NW France, some of the French plateau areas and I would guess too areas like the Pyrenees. The changes that allowed expansion and infilling of areas that were not settled by the more fussy early farmers before 5000BC or so may have included more advanced dairying according to lipid traces on pots, the spread of the abilty to drink milk without processing as well as changes in tools and cerials.

The uncertain question was whether these new middle Neolithic cultures involved a new genetic element. Well the recent paper on lactase persistance does indicate an age and origin point in the south-eastern part of the Old Europe farming world that would be consistent with the expansion of fortune lineages that possessed this. This may have for a long time been a minority, including during its period of spreading, until selective advantage expanded it on a local all over Europe. The question is whether R1b was at least involved in this. I think some of the latest dating ideas that push it back in date a bit would be compatible with this. It cannot be said their is a simple culture and pots trail that marks this out but rather it may have caused transformation in existing cultures and later some offshoots into unsettled territories.

However, I do not think modern levels of lactase persistance should be taken too literally as an indicator of deep time patterns. The selection for lactase persistance would have varied and in areas where it was an advantage and where dairying is crucial this selection would have continued into modern times while in other areas less dairy dependent and where non processed milk was not commonly drunk the selection would have been weaker. Broadly speaking wet, cold and upland areas where dairying was essential and dairy products kept well and where dairying has remained crucial into modern times are the areas where lactase persistence is highest.

Michał
08-05-2013, 07:57 AM
What do you think of the age of R1b-P312 that I recalculated from Wei.et.al.2012
R1b-P312(n=13) Age: 6436 ybp +-953 ybp.

Yes, I agree that your approach seems to make some sense (and it's nice that this estimation is consistent with the results reported by Terry Drobb).

razyn
08-14-2013, 09:53 PM
Earlier on this thread there are some excessively early estimates for the age of M153 -- if we take at all seriously the notion that SNPs occur at a stately pace. Anyway it's now known to be about nine steps (SNPs) farther down the tree than it was 2-3 years ago, at which time various illustrations had it right under P312. However: one of the newly placed SNPs immediately under DF27 (so, arguably pretty old, and in that same phylogeny) is DF81, which is looking more and more like another subclade found primarily in men of Basque patrilineal ancestry. Given its position on the haplotree, it could be a much older SNP than M153 (which most of the people who have been running these TMRCA formulae have now dated less than 2,000 years old). But I don't think enough people have tested DF81 yet for there to be much information available about its variance, interclade or otherwise.

Mikewww
08-14-2013, 10:26 PM
... I have already asked this question in another thread but let me repeat it once more. Are there any reliable STR-based estimations that would suggest that the M269(xL23) (para)group is older than clade L23 (and if so, into how many potential subclades is this group divided)?
No, I've never seen where TMRCA calculations or variance numbers for M269xL23 paragroups that were older/more diverse than L23xL51(probably the Z2103/Z2105 subclade) estimates.

I can only conclude that the M269xL23 remnants are a very limited and somewhat youthful branches. They do not apparently adequately represent the paragroup.


BTW, both Sardinian cases of L21 are DF1+.

Can you tell me how to identify these samples? I've downloaded the supplementary data but would like to look at any detail on these two samples that I could. Thank you in advance. I'm DF1+, aka as L513+. There is one other L513+ from a test at a lab in Italy but no one knows anything about the individual or his MDKA.

Mikewww
08-14-2013, 10:41 PM
Earlier on this thread there are some excessively early estimates for the age of M153 -- if we take at all seriously the notion that SNPs occur at a stately pace. Anyway it's now known to be about nine steps (SNPs) farther down the tree than it was 2-3 years ago, at which time various illustrations had it right under P312. However: one of the newly placed SNPs immediately under DF27 (so, arguably pretty old, and in that same phylogeny) is DF81, which is looking more and more like another subclade found primarily in men of Basque patrilineal ancestry. Given its position on the haplotree, it could be a much older SNP than M153 (which most of the people who have been running these TMRCA formulae have now dated less than 2,000 years old). But I don't think enough people have tested DF81 yet for there to be much information available about its variance, interclade or otherwise.

I was asked to calculate the TMRCAs for the DF27 lineage down to M153. As you probably know, I'm very averse to short haplotypes so I'm only doing this on 67 Y STRs. I'm also avoiding actual TMCRA estimates so I can avoid mutation rate arguments. This is strictly informational, but it does line up like one would think STR diversity should.

I have the DF27 project people loaded in a spreadsheet and can easily calculate Sum of the Variance and Maximum GD to the modal for 67 STR (only) haplotypes. This is just a rough way to look at diversity.

R1b-DF27
Sum of Var: 21.77
Max GD to modal: 29

R1b-Z196>Z196
Sum of Var: 21.41
Max GD to modal: 29

R1b-Z196>Z196>Z209>Z220
Sum of Var: 18.71
Max GD to modal: 26

R1b-P312>DF27>Z196>Z209>Z220>Z216
Sum of Var: 13.85
Max GD to modal: 18

R1b-P312>DF27>Z196>Z209>Z220>Z216>Z278>Z214
Sum of Var: 12.31
Max GD to modal: 13

R1b-P312>DF27>Z196>Z209>Z220>Z216>Z278>Z214>M153
Sum of Var: 8.7
Max GD to modal: 11


Also, here is DF81, but with only 3 haplotypes.

R1b-P312>DF27>DF81
Sum of Var: 9.3
Max GD to modal: 11

DF81 is potentially much more diverse because we don't have knowledge of subclades upstream of it that would "cap" its age. However, we can't really say DF81 is anywhere near as old as DF27 yet. I think DF81 could be quite old because I have "suspects" that are up to GD=20 at 67 from the DF81 suspected modal. However, by that time, we are now including people from Denmark and Germany so it is not necessarily a Basque only marker anymore.

P.S. - Please notice that the DF27 down to M153 numbers are actually some of the anecdotal types of things I've seen in the past when looking at STR diversity and lots of STRs - they seem to have some sense with the SNP based phylogenetic branching (in other words STRs are meaningful.) However, this does not make comparing diversity across geographies any more effective than ever because you could be mixing subclades and different sources.

razyn
08-15-2013, 03:01 AM
R1b-P312>DF27>Z196>Z209>Z220>Z216>Z278>Z214>M153
Sum of Var: 8.7
Max GD to modal: 11


Also, here is DF81, but with only 3 haplotypes.

R1b-P312>DF27>DF81
Sum of Var: 9.3
Max GD to modal: 11

DF81 is potentially much more diverse because we don't have knowledge of subclades upstream of it that would "cap" its age. However, we can't really say DF81 is anywhere near as old as DF27 yet.

That's what I was referring to, but just in case Jean L (or anybody else) thinks I was wildly exaggerating when I guessed at about nine steps from P312 to M153 -- there are several others that are known, but omitted from Mike's list, mainly because FTDNA doesn't offer an a la carte SNP test for them. Some are on the Geno 2 chip. The more complete list might read R1b-P312>Z294>Z274>Z196>Z209>Z220>Z210>Z295>CTS12074>Z216>Z278>M153. I may have Z294/Z274 out of sequence, but they are in that area. And that list, in fact, contains more than nine steps.

Anyway, the point is made more clearly, in my opinion, by the variance (as just described here by Mike). In this specific case, partly because the Basques interest so many people, we have had a lot of people testing (including, but not limited to, WTY and 1000 Genomes). A lot of SNPs have been found in the past 2-3 years, and the M153 one no longer looks anywhere near as old as P312. There isn't as much to be said, yet, about DF81.

P.S. There have been several references to a Terry Drobb; that person's name is actually Terry D. Robb. http://www.goggo.com/terry/HaplogroupI1/

R.Rocca
08-15-2013, 11:53 AM
What we have to be careful of is founder affects. If the first M153 was a powerful chief during the Bronze Age, it will tell us very little about when or where his ancestors came from.

As for phylogeny, let's not forget that the odds were heavily stacked in favor of finding many younger downstream subclades of DF27 from Iberia because we had many more DF27 sample sequences from Iberia or Iberia-by-proxy to compare to one another. If we had 50 complete DF27 sequences from the Low Countries, it could be that we would also find new younger-looking subclades below Z220 that are "Dutch" for example. Then again, we might not, and that is the trick in all of this, finding the area that has the most diversity of upstream clades.

Michał
08-16-2013, 11:20 AM
Can you tell me how to identify these samples? I've downloaded the supplementary data but would like to look at any detail on these two samples that I could.
You will find this information in the supplementary table S1. After downloading and opening the original file, you will see the sheet no. 3 (singletons<4 reads), so you need to go to sheet no. 1 (informative) and then go to the row 10708 (SNP #10707) to see L21. You will also find DF1 (L513) in the next row (#10708). The two Sardinian people who are L21+ DF1+ are individuals marked as 1016 and 1017, respectively. They both share five additional SNPs (#10709-10713) that all seem to be absent in the remaining P312 members. Additionally, individual 1016 shows one “secure” singleton and five singletons with less than 4 reads, while individual 1017 shows three “secure” singletons and 2 singletons with <4 reads. Please let me know if anything is not clear yet.