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Jean M
11-28-2013, 12:11 AM
Unpublished as yet, but looks like it is on its way:

Oddný Ósk Sverrisdóttir et al., A late Neolithic Iberian farmer exhibits genetic affinity to Neolithic Scandinavian farmers and a Bronze Age central European farmer


The spread of farming, the neolithisation process, swept over Europe after the advent of the farming lifestyle in the near east approximately 11,000 years ago. However the mode of transmission and its impact on the demographic patterns of Europe remains largely unknown. In this study we obtained : 66,476,944 bp of genomic DNA from the remains of a 4000 year old Neolithic farmer from the site of El Portalón, 15 km east of Burgos, Spain. We compared the genomic signature of this individual to modern-day populations as well as the few Neolithic individuals that has produced large-scale autosomal data. The Neolithic Portalón individual is genetically most similar to southern Europeans, similar to a Scandinavian Neolithic farmer and the Tyrolean Iceman. In contrast, the Neolithic Portalón individual displays little affinity to two Mesolithic samples from the near-by area, La Brana, demonstrating a distinct change in population history between 7,000 and 4,000 years ago for the northern Iberian Peninsula.

http://www.diva-portal.org/smash/record.jsf?pid=diva2:665597

Jean M
11-28-2013, 12:29 AM
There is a book chapter (in Spanish) available from ResearchGate about the site: El Neolítico en la nueva secuencia estratigráfica del yacimiento del Portalón de Cueva Mayor (Sierra de Atapuerca, Burgos) http://www.researchgate.net/publication/253238562_El_Neoltico_en_la_nueva_secuencia_estrat igrfica_del_yacimiento_del_Portaln_de_Cueva_Mayor_ %28Sierra_de_Atapuerca_Burgos%29

Also there is an attractive poster presentation (again in Spanish), illustrating the use of the site from the Neolithic to the Bronze Age: http://www.diariodeatapuerca.net/PortalonCuevaMayor.pdf

Jean M
11-28-2013, 12:39 AM
I suspect that "genetically most similar to southern Europeans" actually means to Sardinians and Basques. That was a point made by Helena Malmström at the recent Royal Society Ancient DNA meeting. "Ancient farmers look genetically closer to modern Basques and Sardinians (generalising to Southern Europe is a bit unfair)". http://www.anthrogenica.com/showthread.php?1601-Royal-Society-Ancient-DNA-meeting-November-2013-%28tweets-from%29&p=19855&viewfull=1#post19855 . She was talking about the first farmers in Scandinavia, but it all ties up.

Anglecynn
11-28-2013, 02:27 AM
Fascinating. Just corroborates the other findings so far. It's pretty important that the two populations were living nearby for a significant period yet remained so distinct. Especially that there is genetic similarity of hunter gatherers to hunter gatherers and farmers to farmers all the way from Iberia to Scandinavia.

alan
11-28-2013, 11:41 AM
Very interesting although 4000 years old if meant literally is not the Neolithic.

Generalissimo
11-28-2013, 11:57 AM
That's a Chalcolithic farmer, from near present-day Basque Country. I hope they got his Y-DNA, but based on that abstract, it doesn't seem so.

Jean M
11-28-2013, 12:41 PM
Very interesting although 4000 years old if meant literally is not the Neolithic.

Yes I noticed that. Level 9 at the site is Neolithic. Radiocarbon dates for the layer run from around 6000 BC to 4000 BC. Levels 7/8 and 6 are Copper Age. Dates for them: 3340-2920 BC, 2580-2200 BC. So something is wrong in the abstract. Either the farmer is from 4000 BC, or he/she is actually Copper Age.

Generalissimo
11-28-2013, 01:33 PM
Yes I noticed that. Level 9 at the site is Neolithic. Radiocarbon dates for the layer run from around 6000 BC to 4000 BC. Levels 7/8 and 6 are Copper Age. Dates for them: 3340-2920 BC, 2580-2200 BC. So something is wrong in the abstract. Either the farmer is from 4000 BC, or he/she is actually Copper Age.

The term Late Neolithic is often used to describe the Copper Age/Chalcolithic in aDNA papers.

Jean M
11-28-2013, 02:00 PM
That is true David, but usually that is because the archaeologists themselves opt for that term for the culture in question.* In this case the archaeologists have been crystal clear in making the distinction, so it is a bit of a puzzle. It could be that what the Spanish term Copper Age, the Swedish want to call Late Neolithic - the researcher is at Uppsala University.

*Northern European archaeologists tend to avoid the term "Copper Age" and stick to the old "three age" system: Stone, Bronze, Iron. In southern Europe, where the Copper Age really can't be ignored - it is longer and particularly significant in the Balkans - the term gets used.

ADW_1981
11-28-2013, 02:33 PM
Unpublished as yet, but looks like it is on its way:

Oddný Ósk Sverrisdóttir et al., A late Neolithic Iberian farmer exhibits genetic affinity to Neolithic Scandinavian farmers and a Bronze Age central European farmer



http://www.diva-portal.org/smash/record.jsf?pid=diva2:665597

It would be interesting if the sample yields any Caucasus/West Asian component like Oetzi, or any SW Asian like the Swedish sample.

Jean M
01-22-2014, 12:44 PM
We now have a different paper from this research, reported by Richard Rocca over in http://www.anthrogenica.com/showthread.php?97-Genetic-Genealogy-and-Ancient-DNA-in-the-News&p=27997&viewfull=1#post27997

Oddný Ósk Sverrisdóttir et al., Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe, Molecular Biology and Evolution, online ahead on print 21 January 2014.
http://mbe.oxfordjournals.org/content/early/2014/01/20/molbev.msu049.abstract?sid=4795f252-cd25-49c2-bbea-d330d155046f

This paper looks at eight individuals from El Portalón de Cueva Mayor, Spain, from what they term the Late Neolithic to early Bronze Age. (In other words they are avoiding the term Copper Age, as deduced above.) The average date for them is 3,735 cal BP = 1,735 BC.

jeanL
01-22-2014, 03:27 PM
We now have a different paper from this research, reported by Richard Rocca over in http://www.anthrogenica.com/showthread.php?97-Genetic-Genealogy-and-Ancient-DNA-in-the-News&p=27997&viewfull=1#post27997

Oddný Ósk Sverrisdóttir et al., Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe, Molecular Biology and Evolution, online ahead on print 21 January 2014.
http://mbe.oxfordjournals.org/content/early/2014/01/20/molbev.msu049.abstract?sid=4795f252-cd25-49c2-bbea-d330d155046f

This paper looks at eight individuals from El Portalón de Cueva Mayor, Spain, from what they term the Late Neolithic to early Bronze Age. (In other words they are avoiding the term Copper Age, as deduced above.) The average date for them is 3,735 cal BP = 1,735 BC.

So basically a group of individuals from Burgos ~ 1735 BC lacked the LP mutation, we have Loschbour (8000 ybp) and Stuttgart(7500 ybp) (http://biorxiv.org/content/biorxiv/suppl/2013/12/23/001552.DC1/001552-3.pdf) both lacking the LP mutation, then there is the Early Neolithic LBK sample tested by Burger ~ 5000 BC (http://www.pnas.org/content/104/10/3736.full.pdf+html?with-ds=yes), then absent in Avellaner Cardial Catalonia 7000 ybp (http://www.pnas.org/content/early/2011/10/24/1113061108.full.pdf+html?with-ds=yes), then we have SW France Treilles 5000 ybp no LP (26/26 C/C) (http://www.pnas.org/content/early/2011/05/24/1100723108.full.pdf+html?with-ds=yes), then here is where it gets interesting, the Southern Basque sample from SJAPL in Alava dated to 5070±150 ybp and considered to be late neolithic period (http://www.nature.com/ejhg/journal/v20/n7/pdf/ejhg2011254a.pdf) has 4/13 or 21% T/T, 2 T/C or 10.5% and the rest C/C, so it seems 6/19 or ~32% of individuals could drink milk, then right next to them just 500 years later the sample from Longar dated to 4450±70 ybp, that is, Late Neolithic–Early Chalcolithic shows only 1/7 T/T or 14% and no C/T. So the incoming during the Late Neolithic-Early Chalcolithic transition in the southermost areas of the Basque Country there was a reduction in the LP mutation frequency. I say this is interesting because now this Chalcolithic sample from Burgos not too far away from the Basque Country yields no LP mutations, and the SJAPL sample from Alava shows signs of violence in the 100+ individuals buried there. For the sake of completeness the only other ancient sample that has yield a mutation was 1/10 individual from the Pitted Ware Culture (http://www.biomedcentral.com/1471-2148/10/89/) who turned out to be C/T for the -13910*T allele.

So in summary -13910*T allele status:

WHG: Loschbour (8000 ybp) all C/C
LBK+Early Central European Neolithic(7500-5000 ybp): all C/C
Cardial Northeastern(Avellaner) Spain(7000 ybp): all C/C
Late Neolithic SW(Treilles) France (5000 ybp): all C/C
Late Neolithic Southern Basque-Alava(SJAPL) (5000 ybp): 4 T/T, 2 C/T, 13 C/C
Late Neolithic-Early Chalcolithic Southern Navarra(Longar) (4500 ybp): 1 T/T, 6 C/C
Late Neolithic-Early Bronze Age (El Portalón de Cueva Mayor) Northern Spain: 8/8 C/C

Not quite what one would expect from a diffusion of LP via the LBK, Cardial, or even from the so called Stelae people.

Jean M
01-22-2014, 03:58 PM
Not quite what one would expect from a diffusion of LP via the LBK, Cardial, or even from the so called Stelae people.

Certainly not the LBK or Cardial. That has been clear to me for years, regardless of Itan 2009 pushing the idea of diffusion via LBK. It is interesting that this paper accepts that there has been population replacement in central Europe after early Neolithic farming.

On Stelae People I reserve my judgement. We don't have data from their sites. But I do feel that a separate Copper Age pastoralist flow from the Balkans explains present-day Basque LP.

By the way I have a table online for -13910 in aDNA: http://www.ancestraljourneys.org/autosomaladna.shtml

alan
01-22-2014, 04:04 PM
If selective pressures for this began with the spread of dairying (probably taking some centuries to get to a detectable level in any given area) then it should be remembered that that was a post-LBK and post-Cardial migration wave thing in Europe and would not be expected in those cultures. Roughly speaking one would expect selective pressure to commence in SE Europe c. 5500BC, east-central Europe after 5000BC and north, alpine and western Europe c. 4000-3500BC. So, as far as I am concerned, these results are pretty in line with expectations and the appearance of LP in the Basque ones is probably really simply because they are rather late ones from a time when some areas would have been under selection pressure for it for some centuries. There are far too few samples across this large span of time and space to actually pick out the pattern of spread. As well as the time and space element there would also be the additional element that selection pressure would be strongest and quicker to have an impact in areas where dairying was strongly preferred/essential, such as mountain or very wet areas less suitable for other forms of agriculture.

The only question I think remains is whether LP was a thing that was already spread in very low numbers below detection before the period when dairying took off and was subsequently selected for on a local basis when dairying spread or whether there was an actual new long distance gene flow involved.


So basically a group of individuals from Burgos ~ 1735 BC lacked the LP mutation, we have Loschbour (8000 ybp) and Stuttgart(7500 ybp) (http://biorxiv.org/content/biorxiv/suppl/2013/12/23/001552.DC1/001552-3.pdf) both lacking the LP mutation, then there is the Early Neolithic LBK sample tested by Burger ~ 5000 BC (http://www.pnas.org/content/104/10/3736.full.pdf+html?with-ds=yes), then absent in Avellaner Cardial Catalonia 7000 ybp (http://www.pnas.org/content/early/2011/10/24/1113061108.full.pdf+html?with-ds=yes), then we have SW France Treilles 5000 ybp no LP (26/26 C/C) (http://www.pnas.org/content/early/2011/05/24/1100723108.full.pdf+html?with-ds=yes), then here is where it gets interesting, the Southern Basque sample from SJAPL in Alava dated to 5070±150 ybp and considered to be late neolithic period (http://www.nature.com/ejhg/journal/v20/n7/pdf/ejhg2011254a.pdf) has 4/13 or 21% T/T, 2 T/C or 10.5% and the rest C/C, so it seems 6/19 or ~32% of individuals could drink milk, then right next to them just 500 years later the sample from Longar dated to 4450±70 ybp, that is, Late Neolithic–Early Chalcolithic shows only 1/7 T/T or 14% and no C/T. So the incoming during the Late Neolithic-Early Chalcolithic transition in the southermost areas of the Basque Country there was a reduction in the LP mutation frequency. I say this is interesting because now this Chalcolithic sample from Burgos not too far away from the Basque Country yields no LP mutations, and the SJAPL sample from Alava shows signs of violence in the 100+ individuals buried there. For the sake of completeness the only other ancient sample that has yield a mutation was 1/10 individual from the Pitted Ware Culture (http://www.biomedcentral.com/1471-2148/10/89/) who turned out to be C/T for the -13910*T allele.

So in summary -13910*T allele status:

WHG: Loschbour (8000 ybp) all C/C
LBK+Early Central European Neolithic(7500-5000 ybp): all C/C
Cardial Northeastern(Avellaner) Spain(7000 ybp): all C/C
Late Neolithic SW(Treilles) France (5000 ybp): all C/C
Late Neolithic Southern Basque-Alava(SJAPL) (5000 ybp): 4 T/T, 2 C/T, 13 C/C
Late Neolithic-Early Chalcolithic Southern Navarra(Longar) (4500 ybp): 1 T/T, 6 C/C
Late Neolithic-Early Bronze Age (El Portalón de Cueva Mayor) Northern Spain: 8/8 C/C

Not quite what one would expect from a diffusion of LP via the LBK, Cardial, or even from the so called Stelae people.

jeanL
01-22-2014, 04:12 PM
Certainly not the LBK or Cardial. That has been clear to me for years, regardless of Itan 2009 pushing the idea of diffusion via LBK. It is interesting that this paper accepts that there has been population replacement in central Europe after early Neolithic farming.

On Stelae People I reserve my judgement. We don't have data from their sites. But I do feel that a separate Copper Age pastoralist flow from the Balkans explains present-day Basque LP.

By the way I have a table online for -13910 in aDNA: http://www.ancestraljourneys.org/autosomaladna.shtml

Thank you for the table, that would have made my life easier. :)

What do you make of the reduction observed in the Basque Country along the Late Neolithic-Early Chalcolithic period, I mean SJAPL shows 6(4 T/T+2 T/C)/19 individuals with LP alleles at 5000 ybp, just 500 years later in Longar we find only 1/7 T/T. In any case the SJAPL sample isn't Copper Age but late Neolithic, and in fact, it does seem to be a burial from a conflict zone, that is, there are signs of violence in the group burial. So the higher presence of LP allele in SJAPL relative to Longar doesn't suggest a Copper Age pastoralist flow from the Balkans, quite the contrary, one would expect higher values in Longar which is truly Early-Chalcolithic, also, why would SJAPL show LP alleles, while the Treilles people at the same time 5000 ybp lacked it. Why would these Chalcolithic Iberians from Burgos lack it, something doesn't add up!!!

Silesian
01-22-2014, 04:26 PM
Thank you for the table, that would have made my life easier. :)
There is no one like JeanM, she really spoils us with her hard work, her magic is to strong :) !


. So the higher presence of LP allele in SJAPL relative to Longar doesn't suggest a Copper Age pastoralist flow from the Balkans, quite the contrary, one would expect higher values in Longar which is truly Early-Chalcolithic, also, why would SJAPL show LP alleles, while the Treilles people at the same time 5000 ybp lacked it. Why would these Chalcolithic Iberians from Burgos lack it, something doesn't add up!!!

What do you make of rh gene found in Basque and in Pakistan, which way did it flow east to west or vice versa, or from Balkans.
http://www.ayubmed.edu.pk/JAMC/PAST/20-4/Khattak.pdf

Jean M
01-22-2014, 06:36 PM
What do you make of the reduction observed in the Basque Country along the Late Neolithic-Early Chalcolithic period, I mean SJAPL shows 6(4 T/T+2 T/C)/19 individuals with LP alleles at 5000 ybp, just 500 years later in Longar we find only 1/7 T/T.

I try to resist playing numbers with small samples, particularly if the sample is from a single site where the dead could be closely related. In that case they are not necessarily representative of the whole region and period in which they lived.

lgmayka
01-22-2014, 10:55 PM
If selective pressures for this began with the spread of dairying...
Why would one think that? Middle Easterners have been making and eating cheese for thousands of years, and it hasn't made them lactase-persistent. The selective pressure for lactase persistence is more likely to have arisen in a population that found milk-drinking much more useful or practical than cheesemaking.

Besides, your hypothesis merely raises the question of where cheesemaking first became common, an issue that is itself apparently controversial. According to Wikipedia (http://en.wikipedia.org/wiki/History_of_cheese#Earliest_origins):
---
...the earliest secure evidence of cheese making dates back to 5,500 BCE in Kujawy, Poland.
---

I myself find the term dairying to be needlessly ambiguous and confusing, precisely because it blurs the very sharp and extremely pertinent distinction between cheesemaking (in which most of the lactose can be eliminated) and milk-drinking (in which all the lactose is consumed).

newtoboard
01-22-2014, 11:08 PM
Why would one think that? Middle Easterners have been making and eating cheese for thousands of years, and it hasn't made them lactase-persistent. The selective pressure for lactase persistence is more likely to have arisen in a population that found milk-drinking much more useful or practical than cheesemaking.

Besides, your hypothesis merely raises the question of where cheesemaking first became common, an issue that is itself apparently controversial. According to Wikipedia (http://en.wikipedia.org/wiki/History_of_cheese#Earliest_origins):
---
...the earliest secure evidence of cheese making dates back to 5,500 BCE in Kujawy, Poland.
---

I myself find the term dairying to be needlessly ambiguous and confusing, precisely because it blurs the very sharp and extremely pertinent distinction between cheesemaking (in which most of the lactose can be eliminated) and milk-drinking (in which all the lactose is consumed).

Do you have evidence Middle Easterners are not lactose-persistent or is that based on the frequencies of 13910T because other mutations exist.

jeanL
01-23-2014, 03:12 AM
I try to resist playing numbers with small samples, particularly if the sample is from a single site where the dead could be closely related. In that case they are not necessarily representative of the whole region and period in which they lived.

SJAPL is a Burial of 300+ individuals from the IV Millenium BC, and they have been typed from mt-DNA Haplogroups yielding different haplogroups, Longar is a Burial of ~112 indivuduals, again with different mt-dna. See here for more info: http://digital.csic.es/bitstream/10261/10203/1/Verona2.pdf

lgmayka
01-23-2014, 05:51 AM
Do you have evidence Middle Easterners are not lactose-persistent or is that based on the frequencies of 13910T because other mutations exist.
The Turkish milk fiasco (http://www.hurriyetdailynews.com/students-hospitalized-after-free-milk-fiasco.aspx?pageID=238&nID=19836&NewsCatID=341) is (in)famous. Apparently, many people in Turkey, including government officials, simply refuse to admit that the majority of the population is lactose-intolerant.
---
On the first day of a recent government project overseeing the distribution of free milk in state schools, hundreds of students around Turkey were hospitalized after drinking their milk. More than 1,000 students went to hospitals complaining of poisoning in nine cities and a number of towns in Turkey yesterday.

Education Minister Ömer Dinçer said the students had not been poisoned, but “had sensitivities to milk"...
---

This research paper (http://www.biomedcentral.com/1471-2148/10/36) has a table and map of lactase persistence phenotype frequencies (i.e., actual ability to digest lactose, regardless of genotype). The table is downloadable as an Excel spreadsheet. Here are the sample counts and lactase persistence percentages for Middle Eastern populations. Notice that a large percentage of Saudis are lactase-persistent due to a different mutation (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253962/).


AFGHANISTAN Hazara 10 0.20
AFGHANISTAN Mixed urban 34 0.24
AFGHANISTAN Pasha-I 60 0.13
AFGHANISTAN Pashtun 71 0.21
AFGHANISTAN Tajik 79 0.18
AFGHANISTAN Uzbek 16 0.00
IRAN Iranian 21 0.14
ISRAEL Arabs 67 0.19
JORDAN Jordanian Arabs 148 0.25
JORDAN Mediterranean origin Jordanian Arabs 56 0.23
JORDAN Urban/agricultural Jordanian Arabs 162 0.76
KUWAIT Arab Kuwaiti 70 0.53
KUWAIT Asian Kuwaiti 79 0.42
LEBANON Lebanese 74 0.22
PAKISTAN Punjabi 53 0.55
SAUDI ARABIA Arabs 109 0.43
SAUDI ARABIA Bedouin 21 0.81
SAUDI ARABIA Beduin and Urban Saudi 14 0.86
SAUDI ARABIA Yemenites 17 0.53
TURKEY Central Anatolia 104 0.29
TURKEY Eastern Anatolia 122 0.26
TURKEY North Coast of Turkey 64 0.31
TURKEY South Coast of Turkey 54 0.28
TURKEY Turks 30 0.63
TURKEY Western Anatolia and European Turkey 126 0.30

Generalissimo
01-23-2014, 06:49 AM
Certainly not the LBK or Cardial. That has been clear to me for years, regardless of Itan 2009 pushing the idea of diffusion via LBK.

The rapid rise in frequencies of the LP allele in many populations might be a very recent phenomenon.


Investigating lactase persistence in a Medieval German cemetery: A step towards understanding the rise of the European lactase persistence polymorphism (-3910C/T)

Milk and milk products are important foods in European, African, and Middle Eastern societies, but in other parts of the world lactose intolerance predominates. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but in Europe a single nucleotide polymorphism at -13910C/T in the gene MCM6 causes adult lactase persistence (LP). When and where this polymorphism evolved and the process by which it became the majority allele in Europe has been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but current archaeological evidence is ambiguous.

In this study, DNA was extracted from the dentine of 36 individuals excavated at the Medieval (c. AD 1000-1200) cemetery of Dalheim in Germany. After PCR amplification and cloning, successful sequences were obtained for 25 individuals, of which 13 exhibited a European LP genotype (CT or TT).

Previous ancient DNA-based studies on the Neolithic found that the incidence of LP falls below detection levels in most regions. Our research shows that between the Neolithic and Medieval periods, the frequency of LP rose from near 0% to over 50%. Also, given that the frequency of LP genotypes in modern-day Germany is estimated at 78.5%, our results indicate that rather than being stable by the Medieval period, the lactase persistent genotype has continued to increase in frequency over the last 1000 years. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistent trait and its global cultural implications.

Source (http://physanth.org/annual-meeting/82nd-annual-meeting-2013/aapa-meeting-program-2013)


It is interesting that this paper accepts that there has been population replacement in central Europe after early Neolithic farming.

Not complete population replacement though.

alan
01-23-2014, 08:26 AM
I maybe should have been clearer. I meant that dairying as a dominant aspect can be traced using residues on pottery with a cline moving from NW Anatolia c. 6000BC, Bulgaria c. 5500BC and hitting Britain and northern Europe about 4000BC. The interesting thing is that this dairying importance tracks behind the initial spread of farming in southern, eastern and central Europe although it kind of catches up with the farming spread in the north-west.

I am aware that LP is only an advantage where less processing of milk is an advantage. I would say being able to drink unprocessed milk would be especially and advantage when people went a bit more mobile.

Also from personal experience drinking raw milk is nice if it is cold and obviously keeps better in cool climates. I remember when I was a small kid and we didnt yet have a refrigerator that milk was not a very nice option in warm weather - not only does it go off fast but it just is rather unpleasant when warm. I used to refuse milk as a kid until we got a fridge and I suddenly realised its a nice drink when cold. Even without a fridge it was was nice in winter when it had been sitting on the doorstep in the cold - the colder the better. Thats just me though lol


Why would one think that? Middle Easterners have been making and eating cheese for thousands of years, and it hasn't made them lactase-persistent. The selective pressure for lactase persistence is more likely to have arisen in a population that found milk-drinking much more useful or practical than cheesemaking.

Besides, your hypothesis merely raises the question of where cheesemaking first became common, an issue that is itself apparently controversial. According to Wikipedia (http://en.wikipedia.org/wiki/History_of_cheese#Earliest_origins):
---
...the earliest secure evidence of cheese making dates back to 5,500 BCE in Kujawy, Poland.
---

I myself find the term dairying to be needlessly ambiguous and confusing, precisely because it blurs the very sharp and extremely pertinent distinction between cheesemaking (in which most of the lactose can be eliminated) and milk-drinking (in which all the lactose is consumed).

alan
01-23-2014, 08:43 AM
Is it not also a fact that a lot depends on whether it is cattle or sheep/goats milk? Goats milk is much less likely to be a problem. I read that 50% of those who cannot drink cows milk can drink goats milk. So, the kind of livestock suitable/traditional to a given area will also have an impact on this issue. AFAIK the goat/sheep tradition is much stronger in the Med. and SW Asia while cattle was more important in temperate Europe and this increased over time.

The main question I was wondering is whether LP spread as a random thing not yet being selected for in small numbers with the first farmers and was then later selected for locally when milk drinking took off OR did it physically spread at a later date with new people.

Following on my comments about raw milk not being very practical or pleasant in a hot climate, another factor in milk and temperature would be transhumance. People who headed up into the mountains in the summer months would also have benefited from the cooler temperatures in uplands in that part of the year. Mobility of any kind surely favoured drinking raw milk as you wouldnt want to be burdened by having elaborate cheese making processes if you were moving around a lot. Also raw milk is clearly the best return for effort no matter how you look at it.

alan
01-23-2014, 09:08 AM
So, I would day the earliest strong selection for LP would be in areas where cattle predominated and a mobile of seasonal transhumance economy existed. Traditionally northern and mountain areas practices summer transhumance which involved the driving of the cattle up to the summer upland pastures and returning to a lowland area in the winter to the pasture that had been preserved their in the absence of cattle. This approach is also designed so that some crops can be grown in the lowlands in the summer and harvested before the cattle return from the uplands. The cattle can then eat the stubble of the harvested crops and in turn they manure the agriculatural fields. Its a good system for maximising use of land in areas where cattle pastoralism predominates and crop growing is a relatively minor component.

This system still predominated in the Celtic fringes of the isles until only a few centuries ago. Halloween actually originated as a Celtic festival associated with the return of the cattle from the upland pastures to the lowland ones. There were also apparently major assemblies at this time as the population scattered in the uplands returned to concentrate in the lowlands again. Mayday or Beltaine was the reverse and marked the exit from the lowland winter farm to the uplands. There seem to have been rituals involving driving the cattle between fires etc at these times. Its obviously not easy to date the origins of this practice and it varies throughout Europe but it undoubtedly has deep prehistoric roots.

Also worth noting is that a pastoralist cattle system like this based on dairying allows for a five fold population increase in the same acreage of land compared to regiemes where cattle were only kept for meat. So, the appearance of such a system may have conferred a major demographic advantage and allowed for a much larger population. In areas which were not great for arable agriculture to to latitude or altitude this must have been a major impact.

alan
01-23-2014, 11:35 AM
The prevailing notion is that transhumance probably developed in the copper/early Bronze age. Although possibly a little out of date and apparently not aware of Evershed's work showing the mid Neolithic spread of developed dairying, this paper makes a strong case that supports the idea that Balkans transhumance developed around the time of the fall of old Europe. Its a little confusing as it uses slightly odd period terminology and what seem to be uncalibrated dates but the picture is clear enough if you have a grasp of the cultural sequences

http://www.academia.edu/247021/2006_The_Origins_of_Transhumant_Pastoralism_in_Tem perate_Southeastern_Europe_A_Zooarchaeological_Per spective_from_the_Central_Balkans

Anglecynn
01-23-2014, 11:56 AM
Is it not also a fact that a lot depends on whether it is cattle or sheep/goats milk? Goats milk is much less likely to be a problem. I read that 50% of those who cannot drink cows milk can drink goats milk. So, the kind of livestock suitable/traditional to a given area will also have an impact on this issue. AFAIK the goat/sheep tradition is much stronger in the Med. and SW Asia while cattle was more important in temperate Europe and this increased over time.

The main question I was wondering is whether LP spread as a random thing not yet being selected for in small numbers with the first farmers and was then later selected for locally when milk drinking took off OR did it physically spread at a later date with new people.

Following on my comments about raw milk not being very practical or pleasant in a hot climate, another factor in milk and temperature would be transhumance. People who headed up into the mountains in the summer months would also have benefited from the cooler temperatures in uplands in that part of the year. Mobility of any kind surely favoured drinking raw milk as you wouldnt want to be burdened by having elaborate cheese making processes if you were moving around a lot. Also raw milk is clearly the best return for effort no matter how you look at it.

Reminds me of one particular people in Africa (I can't remember who or where off the top my head) that are cattle-herders, and they developed a technique for letting the blood of cattle without killing or seriously injuring them, so that it can be drunk or cooked with, in times of emergency or while travelling. I guess milk has a similar advantage too.

newtoboard
01-23-2014, 02:10 PM
The Turkish milk fiasco (http://www.hurriyetdailynews.com/students-hospitalized-after-free-milk-fiasco.aspx?pageID=238&nID=19836&NewsCatID=341) is (in)famous. Apparently, many people in Turkey, including government officials, simply refuse to admit that the majority of the population is lactose-intolerant.
---
On the first day of a recent government project overseeing the distribution of free milk in state schools, hundreds of students around Turkey were hospitalized after drinking their milk. More than 1,000 students went to hospitals complaining of poisoning in nine cities and a number of towns in Turkey yesterday.

Education Minister Ömer Dinçer said the students had not been poisoned, but “had sensitivities to milk"...
---

This research paper (http://www.biomedcentral.com/1471-2148/10/36) has a table and map of lactase persistence phenotype frequencies (i.e., actual ability to digest lactose, regardless of genotype). The table is downloadable as an Excel spreadsheet. Here are the sample counts and lactase persistence percentages for Middle Eastern populations. Notice that a large percentage of Saudis are lactase-persistent due to a different mutation (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253962/).


AFGHANISTAN Hazara 10 0.20
AFGHANISTAN Mixed urban 34 0.24
AFGHANISTAN Pasha-I 60 0.13
AFGHANISTAN Pashtun 71 0.21
AFGHANISTAN Tajik 79 0.18
AFGHANISTAN Uzbek 16 0.00
IRAN Iranian 21 0.14
ISRAEL Arabs 67 0.19
JORDAN Jordanian Arabs 148 0.25
JORDAN Mediterranean origin Jordanian Arabs 56 0.23
JORDAN Urban/agricultural Jordanian Arabs 162 0.76
KUWAIT Arab Kuwaiti 70 0.53
KUWAIT Asian Kuwaiti 79 0.42
LEBANON Lebanese 74 0.22
PAKISTAN Punjabi 53 0.55
SAUDI ARABIA Arabs 109 0.43
SAUDI ARABIA Bedouin 21 0.81
SAUDI ARABIA Beduin and Urban Saudi 14 0.86
SAUDI ARABIA Yemenites 17 0.53
TURKEY Central Anatolia 104 0.29
TURKEY Eastern Anatolia 122 0.26
TURKEY North Coast of Turkey 64 0.31
TURKEY South Coast of Turkey 54 0.28
TURKEY Turks 30 0.63
TURKEY Western Anatolia and European Turkey 126 0.30


Those are some small sample sizes. Really small. I'm not buying that no Uzbeks have the ability to digest milk or only 18% of Tajiks do. I'm not even buying the 55% for the Punjabi population. Palisto posted a study on that argued otherwise.

alan
01-23-2014, 10:45 PM
I imagine breakfast cereal wont have caught on in places that are not LP seeing as they nearly all involve milk being poured on them. Talking of breakfast, I like fish for breakfast - kippers, smoked salmon etc. The Japanese have a lovely fish with some kind of slightly sweet glaze as one of their classic breakfasts.

jeanL
01-24-2014, 12:25 AM
The rapid rise in frequencies of the LP allele in many populations might be a very recent phenomenon.


Not according to this new study (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0086251)



...In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications.

1261

alan
01-24-2014, 12:36 AM
Maju made an interesting post on Dienekes:

As far as I know, the earliest known sites with the T allele at rs4988235 (causing lactase persistance among most Europeans in dominant Mendelian way) are three early Chalcolithic sites: two nearly contemporary ones in the southernmost Basque Country and another one in Götland.

In Götland (Pitted Ware culture) only 1/20 alleles was T (i.e. 1/10 persons had the CT combo, all the rest being CC and therefore likely lactose intolerants).

In Longar (Navarre, dated to c. 4500 BP) 1/7 individuals was TT, while the other six were CC (intolerant). There were no CT cases.

In San Juan Ante Porta Latinam (SJAPL, Araba, dated to c. 5000 BP), 4/19 were TT, 2/19 were CT, while the remaining 13 were CC.

What I found most interesting in the two Basque southern border sites (see here) was that there are too few cases of CT, strongly suggesting that the two populations (the TT and the CC carriers) were just beginning to mix at that point.

Both sites were war cemeteries it seems (mostly adult males, arrow injuries and arrow points) and their mtDNA is somewhat different from the Basque genetic pool of the Neolithic-to-Modern times (less H and U and more K, J and T/X). Their genetic pool, at least judging on the frequency of K and T/X, did not make it to the overall Basque genetic pool of later times.

It's hard to make extrapolations for the generality of Europe but, in the local context, my impression from this Basque data (one of the two European areas best sampled for aDNA, along with NE Germany) is that two populations were meeting at those military cemeteries of the Chalcolithic Age: a foreign one carrying CC (lactose intolerant) and a local one carrying TT (tolerant). The presumption of who were foreign and who local is made based on the relative discordance of their mtDNA pool with previous and later Basque pools (lots more of K and T/X, most likely T, also modern Basques have very high frequencies of lactose tolerance) but is of course somewhat uncertain.

IF there was at least some level of population replacement triggering the spread of the T allele in much of Europe it may well have begun in the Chalcolithic (all tested Neolithic farmers lack it). After that there may have been some strong selective pressure in the Metal Ages but, like the authors, I find difficult to discern which was it.

That point about there being CC and TT but a lack of CT indicating two populations who had only started to mix in the copper age is interesting. Its also interesting that he suggests that the Basques mt DNA only gained its higher levels of H and U after this sort of period. It kind of suggests to me that the Basques were experiencing new geneflow that differed from their previous Neolithic state and that clearly included both LP and mtDNA. We do not know what the yDNA aspect of these changes were but its mighty tempting to suggest R1b may have started to make an impact.

jeanL
01-24-2014, 12:46 AM
That point about there being CC and TT but a lack of CT indicating two populations who had only started to mix in the copper age is interesting. Its also interesting that he suggests that the Basques mt DNA only gained its higher levels of H and U after this sort of period. It kind of suggests to me that the Basques were experiencing new geneflow that differed from their previous Neolithic state and that clearly included both LP and mtDNA. We do not know what the yDNA aspect of these changes were but its mighty tempting to suggest R1b may have started to make an impact.

Not quite, the early Neolithic Basque aDNA shows more mt-DNA H and mt-DNA U than these southernmost Basque samples, that's what Maju meant, so it is likely that these waves had effect on the Ebro Valley, but not on the inner side of the Basque Country.

http://4.bp.blogspot.com/-FonuDFAof1E/UjM9Z2IGlNI/AAAAAAAACLw/dW1EGBzH5CA/s1600/SequenceBasque.jpg

See here: http://class.csueastbay.edu/anthropologymuseum/2006IA/DNA_PDFS/mtDNA/Izagirre1999.pdf

alan
01-24-2014, 01:01 AM
so that south-west Basque periphery Chalcolithic thing looks like an interlude or local thing where H and U actually fell while T/X and R* appeared and K grew. I dont know much about mtDNA. What do those differences in the Chalcolithic sample compared to the Neolithic sample imply?


Not quite, the early Neolithic Basque aDNA shows more mt-DNA H and mt-DNA U than these southernmost Basque samples, that's what Maju meant, so it is likely that these waves had effect on the Ebro Valley, but not on the inner side of the Basque Country.

http://4.bp.blogspot.com/-FonuDFAof1E/UjM9Z2IGlNI/AAAAAAAACLw/dW1EGBzH5CA/s1600/SequenceBasque.jpg

See here: http://class.csueastbay.edu/anthropologymuseum/2006IA/DNA_PDFS/mtDNA/Izagirre1999.pdf

alan
01-24-2014, 01:08 AM
I dont want to blur the observation Maju made about LP perhaps indicating two groups meeting and just beginning to mix in the chalocolithic by branching out into the mtDNA aspect. I find the point he made about LP interesting in itself and who knows this could have been male driven rather than female so mtDNA may be irrelevant.

newtoboard
01-24-2014, 02:59 AM
My thoughts on the matter of the origin and spread of LP:

I agree with Igmayka that an Anatolian origin for LP is less likely than a Caucasus or steppe one. The Anatolian theory is, to some degree, advocated for on account of high frequencies of LP and R1b in NW Europe and the idea that R1b came from Anatolia. The paper Igmayka posted argues for an origin near the Caucasus and I think there was a paper that Dienekes blogged about that argued LP was selected for in Northwestern Europe very recently. This makes more sense given plenty of the R1b rich populations of the Balkans, West Asia and Southern Europe are nowhere near close to having the same ability to digest milk as NW Europeans. Not to mention this ability seems common enough in Fenno-Scandia where plenty of I1, R1a and N1c can be found. Nor would it explain LP in Asia. And I doubt the likely R1a rich Don-Volga groups were taking wives from the Balkans and Dnieper region. I think a maternal spread from a lineage common to all IE groups (U4 or U5 if LP is native to the steppe) or maternal lineages from the Caucasus (H,K,T?) is more likely although that is speculative on my part. Plus since the frequency does not equal origin argument is used in terms of uniparental markers it should apply here IMO.This theory was also advocated based on the Fulani's R1b frequencies and ability to digest milk. But it is unlikely that this NW Anatolian dairying group, if it carried R1b, would have had V88 members. Like I said before different subclades of a haplogroup often have very contrasting histories. I think Jean said it doesn't fit anyways.

newtoboard
01-24-2014, 03:09 AM
On a related note there seems to have been some evidence found last year that cattle were domesticated 10,000 years ago in NW china. I wonder which group did that. The newspaper headlines argue the Neolithic Chinese but there is no evidence for Neolithic Sino a Tibetan groups in NW China.

alan
01-24-2014, 03:48 AM
It would be interesting to get dates for the LP individuals found in Iberia. Its obviously the wrong end of Europe to easily see a steppe origin. More importantly, are they not a little too old to explain by steppe intrusions given that Yamanaya wasnt west of the Black Sea until 3000BC or a little later. I dont know if the dates Maju quoted are calibrated etc.

parasar
01-24-2014, 03:50 AM
Those are some small sample sizes. Really small. I'm not buying that no Uzbeks have the ability to digest milk or only 18% of Tajiks do. I'm not even buying the 55% for the Punjabi population. Palisto posted a study on that argued otherwise.

http://mbe.oxfordjournals.org/content/29/1/249/F1.large.jpg
Distribution of -13910 C>T in India. Crosses represent sample locations. Colors and color key show the frequency of the -13910*T allele estimated by surface interpolation.
http://mbe.oxfordjournals.org/content/29/1/249.full
"We confirm that the mutation is identical by descent to the European allele and is associated with the same .1 Mb extended haplotype in both populations... All -13910*T alleles in our southern Asian sample (fig. 2) are found on the previously defined European A haplotype background, strongly arguing for a single common origin... However, although the >1-Mb haplotype is found in all -13910*T-carrying populations, the decay patterns are not identical across populations, with the Indian samples exhibiting a markedly ladder-like pattern of decay, whereas Europe, the Near East, and Pakistan are all characterized by a single steep drop of EHH roughly 800 kb from the core region at around position 135.5 Mb on chromosome 2... The earliest evidence of cattle herding in south Asia comes from the Indus River Valley site of Mehrgarh and is dated to ∼7,000 YBP (Meadow 1993), thus postdating the predicted start of the European Neolithic sweep ∼7,500 YBP (Burger et al. 2007; Itan et al. 2009). It is therefore plausible that from Europe, the allele subsequently spread into Central Asia, the Near East, Pakistan, and India"

newtoboard
01-24-2014, 04:01 AM
Frequency of 13910T does not equal percentage of people who can digest milk. 22018A has to be considered too and there are likely local mutations too(local as in local to West, Central and South Asia). My point still stands.

newtoboard
01-24-2014, 04:02 AM
How is Tibet so high in 13910T?

newtoboard
01-24-2014, 04:03 AM
Frequency of 13910T does not equal percentage of people who can digest milk. 22018A has to be considered too and there are likely local mutations too(local as in local to West, Central and South Asia). My point still stands.
You can tell this is true because LP in South Asia peaks in Sindh not Punjab.

parasar
01-24-2014, 04:17 AM
How is Tibet so high in 13910T?

No data points there, therefore useless. It just seems high due to contour interpolation.

newtoboard
01-24-2014, 04:26 AM
I'm leaning towards a maternal spread of this trait. There is no reason to assume that it was spread with male lineages.

alan
01-24-2014, 08:20 AM
Its not impossible but post-Neolithic movements do tend to be interpreted as heavily male. I agree though its worth considering. I suppose one could ask what was the big change in mt lineages in Europe and western Asia in the period where LP seems to take off. In the west and central Europe H expands. I know some have tried to see this as a western bell beaker driven expansion but maybe that is wrong. LP doesnt need to have sprung up anywhere in particular anyway.


Just a thought but could the advantage of LP perhaps related to the weaning stage when babies move off mothers milk? In pre-modern times you would think some sort of soft porridge, cottage cheese or similar made with milk or some sort of yogurts might be useful. Other than that its not clear to me what a baby being weaned off mothers milk would have had - I cannot imagine bread, meats etc would be ideal. Maybe those kind of milk products contributed to infant survival. Just a random thought lol




I'm leaning towards a maternal spread of this trait. There is no reason to assume that it was spread with male lineages.

alan
01-24-2014, 08:44 AM
On the whole though it looks like selection has had a far bigger bearing on LP and that will mask the possibly much fainter trances of diffusion. Has anyone ever compared variance of the gene if that is possible because frequency is clearly more a result of constant selective pressure from ancient until modern times in very pastoral areas. As I posted before, the Med. and many Asian traditions involve goats whose milk can be drink by half of the population who are not LP. I also noted in passing that the inability to drink milk in some humans does not kick in until the age of 5-7 or thereabouts so my weaning idea can be dismissed. Still if some sort of transhumance did operate from the copper age, it would have been handy for individual cattle herders up in the hills to be able tojust drink raw milk. Its not such a big deal if entire families move to summer huts for several months and can make cheese but a more if it was just small groups who drove cattle shorter distances and returned daily or every few days to the homestead in the lowlands (as did happen in some reguimes) it would be incredibly handy to be able to just drink milk. So, the social structure of how transhumance and semi mobile pastoralism could have a bearing on just how hand milk drinking was. I dont imagine vertical trashumance (heading up the hills in the summer) would have allowed for steppe type home on wheels in which cheese etc could be moved. So, perhaps people who could drink milk were actually chosen deliberately to take charge of such transhumance and semi-nomadic pastoralism and others who couldnt stay behind and did arable type work. That sort of thing could be spotted in childhood. In general too that ability may have conferred status as being involved with cattle herding would be higher status than arable working in pastoralist societies. Presumably they were no fools and would have chosen the most suitable people for the job.

alan
01-24-2014, 08:58 AM
This seems to suggest LP is associated with greater height

http://www.ncbi.nlm.nih.gov/pubmed/21909290

rms2
01-24-2014, 09:07 AM
Maju made an interesting post on Dienekes:

As far as I know, the earliest known sites with the T allele at rs4988235 . . .

I know this is a trifling, nit-picking point, but it might involve some confusion for some people, so I will take it up. LP at rs4988235 is indicated by an A allele and not a T. Rs4988235 is read at the opposite side of the double helix from 13910, which is at the same location as rs4988235. Since A is paired with T, and T is the LP allele at 13910, the LP allele on the other side of the double helix (at rs4988235) is A.

I hope that is clear.

The same thing happens in the case of 22018, where the LP allele is A. When read from the opposite side of the double helix the SNP is rs182549, and the "risk" or LP allele is T.

Generalissimo
01-24-2014, 09:08 AM
This seems to suggest LP is associated with greater height

http://www.ncbi.nlm.nih.gov/pubmed/21909290

Milk consumption is. But there might be different reasons for that, including the chemicals fed to the cows that produce milk.

Jean M
01-24-2014, 09:25 AM
The rapid rise in frequencies of the LP allele in many populations might be a very recent phenomenon. Source (http://physanth.org/annual-meeting/82nd-annual-meeting-2013/aapa-meeting-program-2013)

That Kruttli et al paper is now out. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0086251

Their conclusions have changed in the published version. From 18 samples they get a figure of 72% LP, roughly the equivalent of modern day figures in Germany and Austria.

Thanks to JeanL for the tip-off : http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=28282&viewfull=1#post28282

Generalissimo
01-24-2014, 10:36 AM
That Kruttli et al paper is now out. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0086251

Their conclusions have changed in the published version. From 18 samples they get a figure of 72% LP, roughly the equivalent of modern day figures in Germany and Austria.

Thanks to JeanL for the tip-off : http://www.anthrogenica.com/showthread.php?709-New-DNA-Papers&p=28282&viewfull=1#post28282

Nevertheless, considering that the LP gene was present in North Germany 6500 years ago, that leaves plenty of time to reach modern frequencies in that area of Europe.

Jean M
01-24-2014, 01:15 PM
..considering that the LP gene was present in North Germany 6500 years ago...

Not that we know of. The earliest published -13910T is in Sweden 3300-2500 BC = 5300-500 years ago. The earliest reported in Germany is from Lichtenstein Cave, Germany 1000 BC. There is a handy graph in the paper.

1266

Generalissimo
01-24-2014, 01:34 PM
Not that we know of. The earliest published -13910T is in Sweden 3300-2500 BC = 5300-500 years ago. The earliest reported in Germany is from Lichtenstein Cave, Germany 1000 BC. There is a handy graph in the paper.

1266

So how does the presence of the LP allele in Basque country 3000-2500 BC support its origin within an ANE population, considering that Basques are one of the few European groups that can be modeled as EEF/WHG with 0% ANE?

soulblighter
01-24-2014, 02:30 PM
So how does the presence of the LP allele in Basque country 3000-2500 BC support its origin within an ANE population, considering that Basques are one of the few European groups that can be modeled as EEF/WHG with 0% ANE?

Was that allele even part of the dataset extracted succesfully by lazardis? there were only several thousand SNPs.

alan
01-24-2014, 02:46 PM
There just are not enough databpoints to be sure of the timing and nature of how we went from no/below detection levels of LP in the earliest Neolithic to what we have today. IMO selection could have started as soon as dairying with cattle took off and arrived in areas where it became dominant and necessary due to the failure of other aspects of the Neolithic template. For example recent work in Ireland indicates that several aspects of the preconceived Neolithic template were dropped after only a few centuries and a more pastoralist society with increasingly ephemeral settlements developed We know cattle dairying was in the isles from the arrival of farming c. 4000BC. However, it may have only been a few centuries later when a more heavily pastoralist and more mobile living developed that selection for LP may have become strong. In that sort of scenario very low levels of LP may have picked up and started strong selection without further intrusions.

parasar
01-24-2014, 03:34 PM
So how does the presence of the LP allele in Basque country 3000-2500 BC support its origin within an ANE population, considering that Basques are one of the few European groups that can be modeled as EEF/WHG with 0% ANE?

There is no clear connection between -13910T and ANE. ANE was a component of ancestral ASI, and none of the other ancestral ASI components (Native Americans, ENA, ASI proxies, etc.) have much -13910T (many are 0%).

parasar
01-24-2014, 03:48 PM
Was that allele even part of the dataset extracted succesfully for Malt'a boy? there were only several thousand SNPs.

Mal'ta boy "carries the ancestral C allele at rs4988235, and not the T allele that confers lactose persistence in western Eurasians."
http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12736-s1.pdf

Silesian
01-24-2014, 03:59 PM
There is no clear connection between -13910T and ANE. ANE was a component of ancestral ASI, and none of the other ancestral ASI components (Native Americans, ENA, ASI proxies, etc.) have much -13910T (many are 0%).
Look at the hot spots for L.P. and compare rh negative found in Bannu and Sindh same Rh- as the Basque have. Highest frequencies L.P./Rh- in India /Pakistan?

http://www.ayubmed.edu.pk/JAMC/PAST/20-4/Khattak.pdf

Bannu 10.73% rh-
Sindh 8.20% rh-

QUOTE=parasar;28298]http://mbe.oxfordjournals.org/content/29/1/249/F1.large.jpg

Jean M
01-24-2014, 04:46 PM
So how does the presence of the LP allele in Basque country 3000-2500 BC support its origin within an ANE population

Who thinks that -13910T arose in an ANE population? ANE = Palaeolithic Siberian Mal'ta boy. -13910T is not part of the allele package of any of the three main elements of the European gene pool identified by Lazaridis 2013. Not everything will fit into those packages. :) It is a later mutation.

We can guess that it was first selected for among dairy farmers, who spread later than the first wave of European farmers. Since the Sea of Marmara region looks to be the place where intensive dairy farming really took off, it is a good bet for where the first positive selection took place. From there it could move up the Danube into the late Neolithic cultures like the TRB with dairy. It could also go east into Cucuteni, which was heavily dairy, and from there to Yamnaya.

1276

soulblighter
01-24-2014, 04:58 PM
Mal'ta boy "carries the ancestral C allele at rs4988235, and not the T allele that confers lactose persistence in western Eurasians."
http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12736-s1.pdf

My bad...I meant Lazardis not Malt'a boy. jean M already answered my question.

newtoboard
01-24-2014, 05:03 PM
Look at the hot spots for L.P. and compare rh negative found in Bannu and Sindh same Rh- as the Basque have. Highest frequencies L.P./Rh- in India /Pakistan?

http://www.ayubmed.edu.pk/JAMC/PAST/20-4/Khattak.pdf

Bannu 10.73% rh-
Sindh 8.20% rh-

QUOTE=parasar;28298]http://mbe.oxfordjournals.org/content/29/1/249/F1.large.jpg

What does rh- have to do with LP? Can you explain this?

parasar
01-24-2014, 05:30 PM
Look at the hot spots for L.P. and compare rh negative found in Bannu and Sindh same Rh- as the Basque have. Highest frequencies L.P./Rh- in India /Pakistan?

http://www.ayubmed.edu.pk/JAMC/PAST/20-4/Khattak.pdf

Bannu 10.73% rh-
Sindh 8.20% rh-...

Are you saying that there is some correlation between the high lactose tolerance in the Punjab/Haryana (50%+) and their low Rh- (7%), because I'm not seeing in it. Are you indicating a positive or negative correlation?

parasar
01-24-2014, 05:33 PM
Who thinks that -13910T arose in an ANE population? ANE = Palaeolithic Siberian Mal'ta boy. -13910T is not part of the allele package of any of the three main elements of the European gene pool identified by Lazaridis 2013. Not everything will fit into those packages. :) It is a later mutation.

We can guess that it was first selected for among dairy farmers, who spread later than the first wave of European farmers. Since the Sea of Marmara region looks to be the place where intensive dairy farming really took off, it is a good bet for where the first positive selection took place. From there it could move up the Danube into the late Neolithic cultures like the TRB with dairy. It could also go east into Cucuteni, which was heavily dairy, and from there to Yamnaya.

1276

Jean,

Was Motala12 (the one with ANE) was tested for -13910 status?


Edit:

Both [Loschbour and Stuttgart] ancient modern humans are homozygous for the ancestral alleles at the LCTa and LCTb polymorphisms and as a result are predicted to have been unable to digest lactose as adults. The LCTa mutation has been estimated to have first experienced positive selection between 6,256 and 8,683 years ago in central Europe (25). Thus, although the allele is associated with the spread of the LBK culture, it is likely to have been uncommon in early LBK populations, consistent with our results.

Jean M
01-24-2014, 06:32 PM
Jean,

Was Motala12 (the one with ANE) was tested for -13910 status?

Why ask me? I have no inside information. All I know is what is in the Lazaridis paper and its supplements.


The LCTa mutation has been estimated to have first experienced positive selection between 6,256 and 8,683 years ago in central Europe (25). Thus, although the allele is associated with the spread of the LBK culture, it is likely to have been uncommon in early LBK populations, consistent with our results.

They are just citing the Itan et al 2009 model, which the more recent paper by Kruttli tacitly recognises as flawed. One big problem with it was that it used only European data.

rms2
01-24-2014, 06:53 PM
So how does the presence of the LP allele in Basque country 3000-2500 BC support its origin within an ANE population, considering that Basques are one of the few European groups that can be modeled as EEF/WHG with 0% ANE?

Aren't the Basques 11.4% ANE on Extended Data Table 3 of the Lazaridis et al paper?

Basques:

EEF 0.593
WHG 0.293
ANE 0.114

jeanL
01-24-2014, 07:49 PM
Aren't the Basques 11.4% ANE on Extended Data Table 3 of the Lazaridis et al paper?

Basques:

EEF 0.593
WHG 0.293
ANE 0.114

Here is what the authors said about it:




K=14 shows the appearance of a component that is maximized in the Kalash and that is widely distributed in South Asia, the Caucasus, the Near East, and in diminishing strength in Europe. It is absent in Sardinians, Basques, and all ancient Europeans, although it is present in MA1. This component also does not appear in North and East Africa where other West Eurasian admixture is observed. This is consistent with MA1 having contributed some ancestry to present-day Europeans not accounted for by West Eurasian Hunter Gatherers and Early European Farmers. The presence of this component in the Near East contrasts with its absence in Stuttgart, consistent with the widely shared negative f3 (Near East; Stuttgart, MA1) statistics (Table 1) indicating that present-day Near Easterners have been affected by gene flow not present in early Near Eastern migrants into Europe.

[...]

Most Europeans are not a 2-way mixture of Loschbour and Stuttgart

We next attempted to fit individual West Eurasian populations as a mixture of Loschbour and Stuttgart, as representatives of Early European farmers and West European Hunter Gatherers. Fig. 1B suggests that this is not possible, as most Europeans form a cline that cannot be reconciled with such a mixture. Nonetheless, for Sardinians (Extended Data Table 1), the most negative f3-statistic is of the form f3(Test; Loschbour, Stuttgart), which suggests that at least some Europeans may be consistent with having been formed by such a mixture. We thus fit each European population into the topology of Fig. S12.6. Only Basques, Pais_Vasco, and Sardinians, can be fit successfully with this model. Fig. S12.8 shows a successful fit.

[...]

Fig. S12.13 shows the range of values of x that were compatible with each population. While a wide range of possible values is consistent with each population, with the exception of some populations which are consistent with no WHG ancestry (Albanian, Ashkenazi_Jew, Greek, Maltese, Sicilian), and some others consistent with no ANE ancestry (Basque, French_South, Bergamo, Pais_Vasco, Sardinian), most Europeans can only be fit as having both WHG and ANE ancestry. Moreover, even in the case of many populations compatible with no WHG or no ANE ancestry, the best fit (Table S12.7) includes some such ancestry. For example, Basques are compatible with having no ANE ancestry, but according to Table S12.10, the best fit has 0.293 WHG and 0.114 ANE ancestry, for an x ratio of 72%, that is, an intermediate value within the range indicated in Fig. S12.1.

Keyword here is "best fit", it is likely that if Sardinians were fitted as a three way, they too would score some ANE. Likely the ANE in Basque is not really ANE, but simply WHG.

parasar
01-24-2014, 07:57 PM
Why ask me? I have no inside information. All I know is what is in the Lazaridis paper and its supplements.


...

Ah, thanks. I thought you had some additional info as you mentioned - "-13910T is not part of the allele package of any of the three main elements" - I see your third element was MA1.

Jean M
01-24-2014, 08:42 PM
I see your third element was MA1.

Not mine. :) I refer to the three main ancient elements defined by Lazaridis et al 2013.

WHG = Western European Hunter-Gatherers = La Brana + Loschbour

EEF = Early European Farmers = Stuttgart + Skoglund farmers + Otzi

ANE = Ancient North Eurasians = Mal'ta boy + Afontova Gora, Siberia

Obviously a later mutation of any kind could travel within a European or Asian population descended from any one of these elements or a combination of them. The only point I'm making is that -13910T was not already there in the aDNA samples selected to represent these elements.

Generalissimo
01-24-2014, 11:11 PM
Who thinks that -13910T arose in an ANE population? ANE = Palaeolithic Siberian Mal'ta boy. -13910T is not part of the allele package of any of the three main elements of the European gene pool identified by Lazaridis 2013. Not everything will fit into those packages. :) It is a later mutation.

We can guess that it was first selected for among dairy farmers, who spread later than the first wave of European farmers. Since the Sea of Marmara region looks to be the place where intensive dairy farming really took off, it is a good bet for where the first positive selection took place. From there it could move up the Danube into the late Neolithic cultures like the TRB with dairy. It could also go east into Cucuteni, which was heavily dairy, and from there to Yamnaya.

Fair enough. I thought I saw a comment from you somewhere claiming that the LP allele spread with one of the main ANE waves into Europe.


Keyword here is "best fit", it is likely that if Sardinians were fitted as a three way, they too would score some ANE. Likely the ANE in Basque is not really ANE, but simply WHG.

I don't think even the authors are certain of whether Basques have some ANE or not. But it seems that if they do, it's just a trace, while it's almost certain that the Sardinians don't have any.

newtoboard
01-25-2014, 01:50 AM
Anyone see the new Eupedia section on LP and R1b? My thoughts:

I wasn't aware R1b men domesticated cattle since as far as I know cattle were domesticated in West Asia and South Central Asia independently and I wouldn't associate either of these domestications with R1b (and R1a) but an assortment of native West Asian and South Central Asian haplogroups such as J, G, and L. I wasn't aware that R1b tribes of Ukraine and South Russia (like I have said multiple times it makes sense to look for R1b in the Dnieper region, Crimea and Balkans but not in South Russia) were the only ones who had a lifestyle dependent on cattle. Everything I gave read argues that true nomadic steppe lifestyle was found east of the Don and west of it the population was more involved with farming than east of it. Also I would love to know about these R1b and J2 Scythians who surely existed.

newtoboard
01-25-2014, 01:52 AM
What does ANE amount have to with LP? It only takes a few people carrying the alleles for it entering the gene pool of an endogamus population followed be selection for it. Plus they do have some ANE since they have R1b.

ADW_1981
01-25-2014, 02:02 AM
What does ANE amount have to with LP? It only takes a few people carrying the alleles for it entering the gene pool of an endogamus population followed be selection for it. Plus they do have some ANE since they have R1b.

Endogamy can't explain the high incidence among western Europeans. It appears that the people with the LP mutation were part of a new population which entered western Europe. Granted, the extremely high incidence may be a more recent phenomenon.

newtoboard
01-25-2014, 02:08 AM
Endogamy can't explain the high incidence among western Europeans. It appears that the people with the LP mutation were part of a new population which entered western Europe. Granted, the extremely high incidence may be a more recent phenomenon.

I said even if a community is endogamous that small scale admixture plus selection could explain high frequencies of LP. Selection is the major factor at work IMO.

rms2
01-25-2014, 02:16 AM
Anyone see the new Eupedia section on LP and R1b? My thoughts:

I wasn't aware R1b men domesticated cattle since as far as I know cattle were domesticated in West Asia and South Central Asia independently and I wouldn't associate either of these domestications with R1b (and R1a) but an assortment of native West Asian and South Central Asian haplogroups such as J, G, and L. I wasn't aware that R1b tribes of Ukraine and South Russia (like I have said multiple times it makes sense to look for R1b in the Dnieper region, Crimea and Balkans but not in South Russia) were the only ones who had a lifestyle dependent on cattle. Everything I gave read argues that true nomadic steppe lifestyle was found east of the Don and west of it the population was more involved with farming than east of it. Also I would love to know about these R1b and J2 Scythians who surely existed.

I wasn't aware of that either. I thought cattle domestication first occurred about 10k years ago in the Taurus Mountains of Anatolia.

You must be talking about this post (http://www.eupedia.com/forum/threads/29484-The-mystery-of-Lactase-Persistence-%28LP%29-in-Europeans?p=425076&viewfull=1#post425076), right?

newtoboard
01-25-2014, 02:24 AM
I wasn't aware of that either. I thought cattle domestication first occurred about 10k years ago in the Taurus Mountains of Anatolia.

You must be talking about this post (http://www.eupedia.com/forum/threads/29484-The-mystery-of-Lactase-Persistence-%28LP%29-in-Europeans?p=425076&viewfull=1#post425076), right?

Yup. There is a reason why the two major cattle subspecies of Eurasia are called bos Taurus and bos Indicus. They represent the two likely centers of domestication. And I can't see any evidence for R groups being the major player behind these domestications. Maybe R2 for bos indicus.

alan
01-25-2014, 03:42 AM
I have said it before, I respect the major efforts he makes in terms of DNA mapping etc but archaeology is not his strong point. That is a complete nonsense passage he wrote. Maybe he is confusing domestication of cattle with using cattle for dairying but even that doesnt make sense unless he is going for some sort of Anatolian IE model and linking it and R1b with the rise of advanced dairying in Marmara. ASAIK that is not his model so he seems pretty confused.

Generalissimo
01-25-2014, 04:06 AM
What does ANE amount have to with LP? It only takes a few people carrying the alleles for it entering the gene pool of an endogamous population followed be selection for it. Plus they do have some ANE since they have R1b.

Well, a lot of scenarios are possible in theory. But I suppose I'm just going by what's most plausible. The LP allele is present in (pre-Indo-European?) Neolithic Iberia and Funnelbeaker Scandinavia, so linking it explicitly with ANE isn't all that plausible.


I have said it before, I respect the major efforts he makes in terms of DNA mapping etc but archaeology is not his strong point. That is a complete nonsense passage he wrote. Maybe he is confusing domestication of cattle with using cattle for dairying but even that doesnt make sense unless he is going for some sort of Anatolian IE model and linking it and R1b with the rise of advanced dairying in Marmara. ASAIK that is not his model so he seems pretty confused.

He seems to fudge the maps sometimes as well to fit his theories. I actually have hopes for him though, because in the near future more ancient genomes will force him to simply focus on the facts and stop the wild speculations.

I have to admit though, I'm really getting tired of all these discussions about what happened in Europe during the Copper Age, and in particular how R1b fits into the puzzle, because there are so few hard facts to go on. I really can't wait for some large scale studies of ancient genomes from Europe.

newtoboard
01-25-2014, 04:09 AM
He's also wrong about populations who are LP at frequencies of 80% or higher being found only in Northern and Western Europe. Unless Czechs, NW Russians and NW south Asians don't exist. But that bit of misinformation isn't surprising given anything east of Western Iran doesn't exist if you look at some Eupedia maps. There are mtDNA W maps on Eupedia that omit South Asia/Centeal Asia despite the origin and expansion of the oldest and most numerous W clades (and W as a whole) from this region is noted by people who have studied this lineage but a North Caucasus origin was declared for W and mtDNA R1a. As if no West Eurasian haplogroups could have originated or been present in South Asia before the arrival of Indo-Europeans. Somehow yDNA J2b and G2a are from the steppe too. Because they are common to Europeans and South Asians(the Neolithic is common as well).

Sorry for the rant. I just find these conclusions a bit annoying.

But he does make good maps for most of Eurasia so props for that. I am sure they are time consuming to make and it is valuable to have the distribution of a lineage laid out in visual form.

newtoboard
01-25-2014, 04:13 AM
I'm not really linking it with ANE but trying to formulate a theory based on the paper that Igmayka posted arguing for its origin in the Caucasus or steppe and it's widespread distribution across Eurasia.

alan
01-25-2014, 06:48 AM
I feel on present evidence that a Balkans starting point for European LP is the logical conclusion with dispersal going both west and east from there. It just fits the archaeological evidence best. My feeling is it was a rare gene spread at least by secondary waves of farmers c. 5500-4000BC and perhaps even earlier but it only became strongly selected for where cattle dairying was crucial. Selection is a lot less likely to have been present where goats predominated because LP is not required to drink goats milk. Its also less likely to be selected for strongly where crops were the important part of the diet. Cooler temperatures would also be a much more likely place for raw milk to take off and places of higher latitude or altitude seem most likely to me. LP would also have been very useful for mobile groups as it gives the option of the ultimate food on the hoof. IMO the LP friednly factors of cattle, dairy, higher altitude/latitude and mobility varied in term of the timing of coming together across Europe but I would think many areas saw these factors coalesce by 4000BC if not earlier.

Perhaps the cooler drier phase centred on the 5.9 kiloyear event was a major driver. It coincided with the period of the fall of Old Europe, the extension of dairy using farmers into northern Europe and the earlier steppe intrusions, not to mention aridification of the Sahara and parts of Asia. In the Balkans farmers moved into the hills and settlements became more ephemeral. Crops became unreliable etc. In the north of Europe a major expansion of farming (which by now included cattle dairying) northwards was followed by a major population decline c. 3500BC. I believe too that cereal growing decline relative to pastoralism around this time and in areas like Ireland settlements get increasingly ephemeral suggesting more mobility. Again this may have favoured LP selection.

So, there could have been a number of non-migratory reasons for LP selection if it already existed in very low quantities among the farmers.

Jean M
01-25-2014, 12:29 PM
Fair enough. I thought I saw a comment from you somewhere claiming that the LP allele spread with one of the main ANE waves into Europe.

You may be thinking of this post by Newtoboard: www.anthrogenica.com/showthread.php?1832-So-are-the-ANEs-the-root-of-PIE&p=26355#post26355


Is it possible that the 22018A and 13910T alleles are associated with ANE? An argument against it would be lactose persistence is higher in NW Europe. But I think that is based solely on 13910T frequencies and some populations like Finns and Kazakhs have more 22018A.

To which I responded:


ANE = Mal'ta boy, far too early to carry lactase persistence. 13910T hasn't turned up in aDNA until about 3000 BC. http://www.ancestraljourneys.org/autosomaladna.shtml . I feel pretty confident that these two alleles were spread by IE speakers and Uralic speakers along with ANE, but that is much later on, after pastoralism made them useful.

http://www.anthrogenica.com/showthread.php?1832-So-are-the-ANEs-the-root-of-PIE&p=26359&viewfull=1#post26359

To which I would add that these two alleles do not have to be exclusively connected to the speakers of PIE and/or Uralic to spread with them. They only have to be present in those populations.

newtoboard
01-25-2014, 01:12 PM
It might have spread with ANE but that doesn't mean it originated with ANE populations. I think it is more likely it originated in the EEF populations of the North Caucasus and spread maternally into the ANE populations of the steppe.v

alan
01-25-2014, 01:48 PM
The Sredny Stog cranial evidence suggests the farming spread into that culture was stronger on the male side.


It might have spread with ANE but that doesn't mean it originated with ANE populations. I think it is more likely it originated in the EEF populations of the North Caucasus and spread maternally into the ANE populations of the steppe.v

newtoboard
01-25-2014, 02:11 PM
Yea but we don't know if that is where LP originated. Plus I don't put too much value into cranial measurements. Men are prone to developing longer faced phenotypes than women too.

rms2
01-25-2014, 02:25 PM
How much lactose is in horse milk? I have drunk horse milk before. It is sweeter, it seems to me, than cow's or goat's milk. It didn't bother me at all, but I am LP and homozygous at both 13910 and 22018, so it shouldn't have even if it is higher in lactose than cow's milk.

My reason for asking is the thought that LP could have been beneficial for groups that depended more on horse milk than cow's or goat's milk.

lgmayka
01-25-2014, 04:23 PM
How much lactose is in horse milk?
This study (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&cad=rja&ved=0CGoQFjAJ&url=http%3A%2F%2Fhrcak.srce.hr%2Ffile%2F103040&ei=tuPjUrmLNIylsATSy4CIDg&usg=AFQjCNGCmC2JpVimcokilgLQe3XSN10qGQ&sig2=EtBUfVdidOvyreY-24IR2Q) compared the constituents of milk from various sources:

Lactose (g/kg), mean from published sources
-----
Mare 63.7
Cow 48.8
Sheep 49
Goat 47
Human 67.0

rms2
01-25-2014, 07:01 PM
This study (https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&cad=rja&ved=0CGoQFjAJ&url=http%3A%2F%2Fhrcak.srce.hr%2Ffile%2F103040&ei=tuPjUrmLNIylsATSy4CIDg&usg=AFQjCNGCmC2JpVimcokilgLQe3XSN10qGQ&sig2=EtBUfVdidOvyreY-24IR2Q) compared the constituents of milk from various sources:

Lactose (g/kg), mean from published sources
-----
Mare 63.7
Cow 48.8
Sheep 49
Goat 47
Human 67.0

Wow, thanks, Larry!

So horse milk is actually quite a bit higher in lactose than all of the other usual sources, nearly 31% higher than that of cows. That means if you had a people who were milking mares and drinking their milk as much or more than that of cows, LP would be even more of a necessity or at least an advantage.

So, what about early steppe peoples? Are there indications they were drinking mares' milk instead of cows' milk or drinking it at least to some extent?

I know Kazakhs use mares' milk, but they often ferment it to make kumis. The yeast that creates alcohol would consume much of the lactose, no doubt. I have also had kumis, both the commercial and homemade varieties. Real, homemade Kazakh kumis tastes like alcoholic blue cheese. It's an acquired taste, for sure.

Milking a mare in Kyrgyzstan.

1282

newtoboard
01-25-2014, 07:05 PM
According to Herodotus Scythians did drink horse milk and making cheese out of it too.

rms2
01-25-2014, 07:15 PM
So, with horse milk at about 31% more lactose than cow's milk and goat's milk, there would be even more selective advantage to LP among horse milk drinking populations. Maybe LP arose among such a population?

newtoboard
01-25-2014, 07:20 PM
So, with horse milk at about 31% more lactose than cow's milk and goat's milk, there would be even more selective advantage to LP among horse milk drinking populations. Maybe LP arose among such a population?

Yea but this seems to be a feature of the Kazakh steppe as it was likely present in Botai and then Scythians and Turks. I don't think there is much evidence for this drinking of horse milk west of the Urals so it is likely too east. I do wish we knew the level of LP in the steppe post Yamnaya as Turks are probably less LP than the previous inhabitants.

rms2
01-25-2014, 07:27 PM
Yea but this seems to be a feature of the Kazakh steppe as it was likely present in Botai and then Scythians and Turks. I don't think there is much evidence for this drinking of horse milk west of the Urals so it is likely too east. I do wish we knew the level of LP in the steppe post Yamnaya as Turks are probably less LP than the previous inhabitants.

I seem to recall from reading Anthony that the Botai and others farther east were foragers who learned horse keeping from their western steppe neighbors. I could be mistaken about that, though, so I'll have to try to find that in Anthony's book. Weren't the steppe people keeping and herding horses before they acquired cattle?

newtoboard
01-25-2014, 08:11 PM
I don't remember that but you are probably but it seems that horse milk consumption was more likely to be prevalent in Botai, if they consumed milk, due to the dominance of horse bones at Botai sites. The steppe west of the Don seemed to be more agricultural (so shhs and goats were likely important) and east of it cattle seemed more important. Is it possible that the shift to cow and goat milk could have reduced the frequencies of LP even if the older population of the European steppe drank horse milk?

rms2
01-25-2014, 08:25 PM
I tried looking through Anthony's book for references to the Botai people learning horse keeping from their western neighbors, but I couldn't find anything, so maybe I was misremembering.

Jean M
04-23-2014, 09:01 PM
Returning to the initial topic of this thread, the genome of a late Neolithic Iberian farmer, we now have another dissertation covering it available, as mentioned by R. Rocca over in the news thread: http://www.anthrogenica.com/showthread.php?97-Genetic-Genealogy-and-Ancient-DNA-in-the-News/page4&p=38167#post38167

http://www.diva-portal.org/smash/get/diva2:667495/FULLTEXT01.pdf

The news is that it gives an mtDNA as well for the El Portalón individual - U5b1b. Also a PCA plot, comparing this sample autosomally with other aDNA samples. It comes closest to modern Tuscans.

1769

rokousa
08-14-2014, 07:09 AM
It comes closest to modern Tuscans.

yeah....both have near eastern origin...
Tuscany was invaded (522-1222 ad) by West Asians (45%) and small group of western Europeans. (Hellenthal 2014)......modern Tuscans?

Jean M
09-07-2015, 09:09 PM
http://www.bbc.co.uk/news/science-environment-34175224
Ancient DNA cracks puzzle of Basque origins


DNA from ancient remains seems to have solved the puzzle of one of Europe's most enigmatic people: the Basques.

The distinct language and genetic make-up of the Basque people in northern Spain and southern France has puzzled anthropologists for decades. One theory proposed that they were an unmixed pocket of indigenous hunters. Now, a study in PNAS journal suggests they descend from early farmers who mixed with local hunters before becoming isolated for millennia.

The Basques have unique customs and a language - Euskera - that is unrelated to any other spoken in Europe, or indeed the world. Nestled in a mountainous corner of Atlantic Europe, they also show distinct genetic patterns to their neighbours in France and Spain. It seemed logical that they were representatives of an older layer of population settlement, but just how far back their roots went has been a topic of debate.

Mattias Jakobsson from Uppsala University in Sweden analysed the genomes of eight Stone Age human skeletons from El Portalón in Atapuerca, northern Spain. These individuals lived between 3,500 and 5,500 years ago, after the transition to farming in southwest Europe. The results show that these early Iberian farmers are the closest ancestors to present-day Basques.

Go west

Comparisons with other ancient European farmers show that agriculture was brought to Iberia by the same migrant groups that introduced it to central and northern Europe. These pioneers expanded from a homeland in the Near East, sweeping across Europe about 7,000 years ago to usher in the period known as the Neolithic. Once the farmers settled down, they mixed with local hunter-gatherers - the descendants of people who lived in Europe during the last Ice Age. Indeed, the El Portalón individuals had more hunter-gatherer ancestry than pioneer farmers from Germany, Hungary and Spain who lived several thousand years earlier.

The new study also goes some way to explaining some of the differences between the Basques and their neighbours in France and Spain. After the initial farmer-hunter mixture was set, the ancestors of the Basques became isolated from surrounding groups - perhaps due to a combination of geography and culture. "It's hard to speculate, but we've been working with Basque historians and it's clear from the historical record that this area was very difficult to conquer," Prof Jakobsson told BBC News. This means the Basque area was largely unaffected by subsequent migrations that shaped genetic patterns elsewhere in Europe.
Migration and isolation

One of these movements occurred in the Bronze Age, when pastoralists from the Steppe - on the eastern periphery of the continent - travelled west en masse. This migration probably spread Indo-European languages across Europe, affecting the central and northern parts of the continent to a greater extent than the south. While the genomes of French and Spanish individuals showed evidence of this eastern genetic input, those of Basques did not.

The paper itself does not seem to be available from PNAS yet.

Jean M
09-07-2015, 09:12 PM
See also http://phys.org/news/2015-09-ancient-genomes-link-early-farmers.html

Ancient genomes link early farmers to Basques


An international team led by researchers at Uppsala University reports a surprising discovery from the genomes of eight Iberian Stone-Age farmer remains. The analyses revealed that early Iberian farmers are the closest ancestors to modern-day Basques, in contrast previous hypotheses that linked Basques to earlier pre-farming groups.

The team could also demonstrate that farming was brought to Iberia by the same/similar groups that migrated to northern and central Europe and that the incoming farmers admixed with local, Iberian hunter-gather groups, a process that continued for at least 2 millennia.

The study is published today, ahead of print, in the leading scientific journal Proceedings of the National Academy of Sciences.

Most of the previous studies about the transition from small and mobile hunter-gatherer groups to larger and sedentary farming populations have focused on central and northern Europe, however much less in known about how this major event unfolded in Iberia. This time, the research team investigated eight individuals associated with archaeological remains from farming cultures in the El Portalón cave from the well-known Anthropological site Atapuerca in northern Spain.

"The El Portalon cave is a fantastic site with amazing preservation of artefact material," says Dr. Cristina Valdiosera of Uppsala University and La Trobe University, one of the lead authors.

5835

alan
09-07-2015, 09:23 PM
See also http://phys.org/news/2015-09-ancient-genomes-link-early-farmers.html

Ancient genomes link early farmers to Basques


5835

Makes sense. One question though. They are highlighting the inaccessibility of the Pyrenees. However, the Aquitani were not located on such difficult land AFAIK.

J Man
09-07-2015, 09:26 PM
Returning to the initial topic of this thread, the genome of a late Neolithic Iberian farmer, we now have another dissertation covering it available, as mentioned by R. Rocca over in the news thread: http://www.anthrogenica.com/showthread.php?97-Genetic-Genealogy-and-Ancient-DNA-in-the-News/page4&p=38167#post38167

http://www.diva-portal.org/smash/get/diva2:667495/FULLTEXT01.pdf

The news is that it gives an mtDNA as well for the El Portalón individual - U5b1b. Also a PCA plot, comparing this sample autosomally with other aDNA samples. It comes closest to modern Tuscans.

1769

U5b1b makes good sense. Could be from a Mesolithic Iberian hunter-gatherer ancestress who was assimilated into Neolithic society.

Jean M
09-07-2015, 09:28 PM
the Aquitani were not located on such difficult land AFAIK.

You have put your finger on the big snag with the argument. I have no trouble believing that the present-day Basques have a similar genetic mixture to the Neolithic people of El Portalon i.e. WHG + EEF. But that does not mean that the people of El Portalon were the direct ancestors of the Basques.

Jean M
09-07-2015, 09:48 PM
Here is the press release from Uppsala University: http://www.uu.se/en/media/press-releases/press-release/?id=2816&area=3,8&typ=pm&lang=en

It states that the paper is Günther et al. (2015) Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques, PNAS.


Ancient genomes link early farmers to Basques

An international team led by researchers at Uppsala University reports a surprising discovery from the genomes of eight Iberian Stone-Age farmer remains. The analyses revealed that early Iberian farmers are the closest ancestors to modern-day Basques, in contrast previous hypotheses that linked Basques to earlier pre-farming groups.

The team could also demonstrate that farming was brought to Iberia by the same/similar groups that migrated to northern and central Europe and that the incoming farmers admixed with local, Iberian hunter-gather groups, a process that continued for at least 2 millennia....

From these individuals who lived 3,500-5,500 years ago, the authors generated the first genome-wide sequence data from Iberian ancient farmers and observed that these share a similar story to those of central and northern Europe. That is, they originate from a southern wave of expansion, and also admixed with local hunter-gatherer populations and spread agricultural practices through population expansions. The authors noticed that although they share these similarities with other European farmers, this early Iberian population has its own particularities...

Our results show that the Basques trace their ancestry to early farming groups from Iberia, which contradicts previous views of them being a remnant population that trace their ancestry to Mesolithic hunter-gatherer groups,” says Prof. Mattias Jakobsson of Uppsala University, who headed the study.

“The difference between Basques and other Iberian groups is these latter ones show distinct features of admixture from the east and from north Africa.” he continues.

alan
09-07-2015, 09:51 PM
It is interesting that Strabo thought the proto-Basque speaking Aquitani were more like Iberians than Gauls.

Next, I must discuss the Aquitani, and the tribes which have been included within their boundaries,68 namely, the fourteen Galatic tribes which inhabit the country between the Garumna and the Liger, some of which reach even to the river-land of the Rhone and to the plains of Narbonitis.

For, speaking in a general way, the Aquitani differ from the Galatic race in the build of their bodies as well as in their speech; that is, they are more like the Iberians.

Their country is bounded by the Garumna River, since they live between this and the Pyrenees. There are more than twenty tribes of the Aquitani, but they are small and lacking in repute; the majority of the tribes live along the ocean, while the others reach up into the interior and to the summits of the Cemmenus Mountains, as far as the Tectosages.

But since a country of this size was only a small division, they added to it the country which is between the Garumna and the Liger. These rivers are approximately parallel to the Pyrenees and form with the Pyrenees two parallelograms, since they are bounded on their other sides by the ocean and the Cemmenus Mountains. And the voyage on either of the rivers is, all told, two thousand stadia.

The Garumna, after being increased by the waters of three rivers, discharges p215its waters into the region that is between those Bituriges that are surnamed "Vivisci" and the Santoni — both of them Galatic tribes; for the tribe of these Bituriges is the only tribe of different race that is situated among the Aquitani; and it does than pay tribute to them, though it has an emporium, Burdigala, which is situated on a lagoon that is formed by the outlets of the river. The Liger, however, discharges its waters between the Pictones and the Namnitae. Formerly there was an emporium on this river, called Corbilo, with respect to which Polybius, calling to mind the fabulous stories of Pytheas, has said: "Although no one of all the Massiliotes who conversed with Scipio72 was able, when questioned by Scipio about Britain, to tell anything worth recording, nor yet any one of the people from Narbo or of those from Corbilo, though these were the best of all the cities in that country, still Pytheas had the hardihood to tell all those falsehoods about Britain." The city of the Santoni, however, is Mediolanium.

Now the most of the ocean-coast of the Aquitani is sandy and thin-soiled, thus growing millet, but it is rather unproductive in respect of the other products. Here too is the gulf which, along with that Galatic Gulf which is within the coastline of Narbonitis, forms the isthmus (itself too, like the latter gulf, having the name "Galatic"). The gulf is held by the Tarbelli, in whose land the gold mines are most important of all; for in pits dug only to a slight depth they find slabs of gold as big as the hand can hold, which at times require but little refining; but the rest is gold p217dust and nuggets, the nuggets too requiring no great amount of working. The interior and mountainous country, however, has better soil: first, next to the Pyrenees, the country of the "Convenae" (that is, "assembled rabble"),73 in which are the city of Lugdunum and the hot springsa of the Onesii74 — most beautiful springs of most potable waters; and, secondly, the country of the Auscii also has good soil.

2 Those tribes between the Garumna and the Liger that belong to Aquitania are, first, the Elui, whose territory begins at the Rhodanus, and then, after them, the Vellavii, who were once included within the boundaries of the Arverni, though they are now ranked as autonomous;75 then the Arverni, the Lemovices, and the Petrocorii; and, next to these, the Nitiobriges, the Cadurci, and those Bituriges that are called "Cubi";76 and, next to the ocean, both the Santoni and the Pictones, the former living along the Garumna, as I have said, 191the latter along the Liger; but the Ruteni and the Gabales closely approach Narbonitis. Now among the Petrocorii there are fine iron-works, and also among the Bituriges Cubi; among the Cadurci, linen p219factories; among the Ruteni, silver mines; and the Gabales, also, have silver mines. The Romans have given the "Latin right"77 to certain of the Aquitani just as they have done in the case of the Auscii and the Convenae.

alan
09-07-2015, 10:12 PM
It is interesting that Strabo thought the proto-Basque speaking Aquitani were more like Iberians than Gauls.

Next, I must discuss the Aquitani, and the tribes which have been included within their boundaries,68 namely, the fourteen Galatic tribes which inhabit the country between the Garumna and the Liger, some of which reach even to the river-land of the Rhone and to the plains of Narbonitis.

For, speaking in a general way, the Aquitani differ from the Galatic race in the build of their bodies as well as in their speech; that is, they are more like the Iberians.

Their country is bounded by the Garumna River, since they live between this and the Pyrenees. There are more than twenty tribes of the Aquitani, but they are small and lacking in repute; the majority of the tribes live along the ocean, while the others reach up into the interior and to the summits of the Cemmenus Mountains, as far as the Tectosages.

But since a country of this size was only a small division, they added to it the country which is between the Garumna and the Liger. These rivers are approximately parallel to the Pyrenees and form with the Pyrenees two parallelograms, since they are bounded on their other sides by the ocean and the Cemmenus Mountains. And the voyage on either of the rivers is, all told, two thousand stadia.

The Garumna, after being increased by the waters of three rivers, discharges p215its waters into the region that is between those Bituriges that are surnamed "Vivisci" and the Santoni — both of them Galatic tribes; for the tribe of these Bituriges is the only tribe of different race that is situated among the Aquitani; and it does than pay tribute to them, though it has an emporium, Burdigala, which is situated on a lagoon that is formed by the outlets of the river. The Liger, however, discharges its waters between the Pictones and the Namnitae. Formerly there was an emporium on this river, called Corbilo, with respect to which Polybius, calling to mind the fabulous stories of Pytheas, has said: "Although no one of all the Massiliotes who conversed with Scipio72 was able, when questioned by Scipio about Britain, to tell anything worth recording, nor yet any one of the people from Narbo or of those from Corbilo, though these were the best of all the cities in that country, still Pytheas had the hardihood to tell all those falsehoods about Britain." The city of the Santoni, however, is Mediolanium.

Now the most of the ocean-coast of the Aquitani is sandy and thin-soiled, thus growing millet, but it is rather unproductive in respect of the other products. Here too is the gulf which, along with that Galatic Gulf which is within the coastline of Narbonitis, forms the isthmus (itself too, like the latter gulf, having the name "Galatic"). The gulf is held by the Tarbelli, in whose land the gold mines are most important of all; for in pits dug only to a slight depth they find slabs of gold as big as the hand can hold, which at times require but little refining; but the rest is gold p217dust and nuggets, the nuggets too requiring no great amount of working. The interior and mountainous country, however, has better soil: first, next to the Pyrenees, the country of the "Convenae" (that is, "assembled rabble"),73 in which are the city of Lugdunum and the hot springsa of the Onesii74 — most beautiful springs of most potable waters; and, secondly, the country of the Auscii also has good soil.

2 Those tribes between the Garumna and the Liger that belong to Aquitania are, first, the Elui, whose territory begins at the Rhodanus, and then, after them, the Vellavii, who were once included within the boundaries of the Arverni, though they are now ranked as autonomous;75 then the Arverni, the Lemovices, and the Petrocorii; and, next to these, the Nitiobriges, the Cadurci, and those Bituriges that are called "Cubi";76 and, next to the ocean, both the Santoni and the Pictones, the former living along the Garumna, as I have said, 191the latter along the Liger; but the Ruteni and the Gabales closely approach Narbonitis. Now among the Petrocorii there are fine iron-works, and also among the Bituriges Cubi; among the Cadurci, linen p219factories; among the Ruteni, silver mines; and the Gabales, also, have silver mines. The Romans have given the "Latin right"77 to certain of the Aquitani just as they have done in the case of the Auscii and the Convenae.

So the majority of the actual Aquitani tribes lived along the Ocean according to Strabo, albeit this is by all accounts a treacherous area for boats that mariners tend to avoid if possible.

It is interesting that when the Romans came they stood out from the rest of the people's of Gaul not only linguistically but also phenotypically. That is as good as saying their automosal mix was different and stood out as unusual in Gaul and more akin to the Iberians. So rather than ask what made the Aquitani distinct, we may ask what was added to the rest of the population of Gaul which made them different to the Aquitani. Part of the key to the Aquitani's difference may be that they were located on a dangerous bit of coast avoided by the beaker people as this map (one of many variants on the web) shows.

http://gallaic.com/BellBeakerNodes.jpg

Even in later times - as late as the Roman's establishment of a light house at A'Coruna, it seems like sea traffic avoided the Bay of Biscay and preferred to head direct between NW France and NW Iberia.

So it seem that the area running from the Garronne into the Spanish Basque country was isolated mostly in the sense of sea traffic and peoples who used the trade routes rather than isolated up the Pyrenees. That surely is the real root of this area remaining genetically somewhat distinct and of course the Basque language still remaining in part of the area.

R.Rocca
09-08-2015, 12:57 AM
See also http://phys.org/news/2015-09-ancient-genomes-link-early-farmers.html

Ancient genomes link early farmers to Basques


5835

Looks like the Copper and Bronze Age samples had, unlike Mesolithic Iberians, light kin and dark eyes. They were also lactose intolerant...


Pero, a pesar de presentar similitudes con otros agricultores europeos, esta población ibérica tiene ciertas particularidades: “Los agricultores de la Edad del Cobre y la Edad del Bronce eran intolerantes a la lactosa al igual que los cazadores recolectores del Mesolítico que habitaban en la Península; sin embargo, a diferencia de estos, tenían la piel más clara y el color de sus ojos era más oscuro”, detalla Valdiosera, también investigadora en la universidad sueca.

Krefter
09-08-2015, 04:34 AM
Unusual ‘relic language’ comes from small group of farmers isolated for thousands of years (http://news.sciencemag.org/archaeology/2015/09/unusual-relic-language-comes-small-group-farmers-isolated-thousands-years):

Interesting quotes:

Modern-day Basques do not show genetic mixing from these later migrants, whose genes contribute between 10% and 25% of the genomes of non-Basques living in the Iberian Peninsula of Spain and Portugal today. “The El Portalon individuals, very similar to the Basques, do not show this additional genetic material,” Jakobsson says.


But today’s Basques turned out to be more closely related to the El Portalón farmers than to any other group in the study, including early hunter-gatherer genomes.

Generalissimo
09-08-2015, 07:16 AM
Raw data is here...

http://www.ebi.ac.uk/ena/data/view/ERP010927

Krefter
09-08-2015, 07:23 AM
Raw data is here...

http://www.ebi.ac.uk/ena/data/view/ERP010927

What time periods are the males from? Are they of good coverage?

Generalissimo
09-08-2015, 07:31 AM
What time periods are the males from? Are they of good coverage?

No idea. I don't have the bandwidth. You should e-mail Felix about these samples.

vettor
09-08-2015, 07:51 AM
Returning to the initial topic of this thread, the genome of a late Neolithic Iberian farmer, we now have another dissertation covering it available, as mentioned by R. Rocca over in the news thread: http://www.anthrogenica.com/showthread.php?97-Genetic-Genealogy-and-Ancient-DNA-in-the-News/page4&p=38167#post38167

http://www.diva-portal.org/smash/get/diva2:667495/FULLTEXT01.pdf

The news is that it gives an mtDNA as well for the El Portalón individual - U5b1b. Also a PCA plot, comparing this sample autosomally with other aDNA samples. It comes closest to modern Tuscans.

1769

with your right map, we can easily envisage that ancient Tuscans and Basques are the "same tribe"..............do we have any similar markers?

Rafe
09-08-2015, 10:23 AM
Are they having steppe or steppe-derived comparison samples? Because this quote is weird:


Modern-day Basques do not show genetic mixing from these later migrants, whose genes contribute between 10% and 25% of the genomes of non-Basques living in the Iberian Peninsula of Spain and Portugal today. “The El Portalon individuals, very similar to the Basques, do not show this additional genetic material,” Jakobsson says.

The part in bold is even weirder. It implies that, because the El Portalón samples lacked that additional admixture, it means Basques themselves lack it, too. It doesn't work like that, even if the two groups are closely related. Didn't Haak et al. estimate that 1/3 of the Basque genome came from the steppes, after all?

genetiker
09-08-2015, 02:01 PM
I'm posting the Y-SNP calls here:

Y-SNP calls from Copper and Bronze Age Spain (https://genetiker.wordpress.com/2015/09/08/y-snp-calls-from-copper-and-bronze-age-spain/)

razyn
09-08-2015, 02:22 PM
I'm posting the Y-SNP calls here:

Is it possible to distinguish dates for the individual samples? Identifying ATP3 as M269 would be a lot more interesting if he's 3500 BC than if he's 1500 BC.

MfA
09-08-2015, 02:25 PM
I'm posting the Y-SNP calls here:

Y-SNP calls from Copper and Bronze Age Spain (https://genetiker.wordpress.com/2015/09/08/y-snp-calls-from-copper-and-bronze-age-spain/)

M269 woot

http://weknowgifs.com/wp-content/uploads/2013/03/it-crowd-popcorn-gif.gif

parasar
09-08-2015, 02:34 PM
I'm posting the Y-SNP calls here:

Y-SNP calls from Copper and Bronze Age Spain (https://genetiker.wordpress.com/2015/09/08/y-snp-calls-from-copper-and-bronze-age-spain/)

How old is ATP3? Is this the same sample? -13,910* C,C http://mbe.oxfordjournals.org/content/early/2014/01/20/molbev.msu049.full.pdf
If these were early farmers, ie, only influenced by hunter-gathers, but not by later 5000ybp farmers, does this mean that either the early farmers or hunter-gathers (this looks unlikely) had M269?

razyn
09-08-2015, 03:04 PM
Looks to me as if the highlighted data show Y3545 (one of many M479 equivalents); and that's R2, not R1b-M269. Am I misunderstanding what is meant by the highlighting?

parasar
09-08-2015, 03:20 PM
Looks to me as if the highlighted data show Y3545 (one of many M479 equivalents); and that's R2, not R1b-M269. Am I misunderstanding what is meant by the highlighting?

That is inconsistent with R1.
The consistent reads would be:
R1b1-L389-P297-FGC46/Y97
R1b1-L389-P297-M269-PF6518

Though I have thought R2 could be a possibility too.
"trace amounts among Europeans - Portugal, Spain, Russia/Bashkort, Italy, Ossetia"
http://www.anthrogenica.com/showthread.php?5179-In-what-archealogical-cltures-wll-the-ancestors-of-R1a-L657-and-R1a-Tarim-be-found/page2&p=102855#post102855

ArmandoR1b
09-08-2015, 03:33 PM
What time periods are the males from? Are they of good coverage?
Based on what was usable for autosomal DNA from the Allentoft samples the BAM files need to be more than 2.3 GB because RISE386 SAMEA3325361 2.3 GB from http://www.ebi.ac.uk/ena/data/view/PRJEB9021 didn't have enough coverage according to http://www.y-str.org/p/ancient-dna.html but RISE94 SAMEA3325340 2.7 GB did.

Neolithic levels (IV-V millennium BC) per http://www.iphes.cat/la-sierra-de-atapuerca

This is what I found for the El Portalón cave (Atapuerca, Spain) samples -

SAMEA3477466 ATP2 12.4 GB
SAMEA3477467 ATP3 81 MB
SAMEA3477469 ATP7 131 MB
SAMEA3477470 ATP9 1.1 GB
SAMEA3477471 ATP16 3.0 GB
SAMEA3477472 ATP17 83.6 MB
SAMEA3477473 ATP20 44.5 MB
SAMEA3477474 Matojo 3.3 GB

http://www.ebi.ac.uk/ena/data/view/ERP010927

So only 3 of those 8 samples are good coverage autosomal.

parasar
09-08-2015, 03:46 PM
We should know soon, since both Y and mtDNA apparently informed the paper's conclusions.
https://www.genomeweb.com/sequencing-technology/ancient-dna-study-suggests-basques-descended-early-iberian-farmers

Chalcolithic El Portalón individuals, named after a cave in Sierra de Atapuerca, Spain, where their remains were found, were tested using low-coverage genome sequencing, mitochondrial genome sequencing, and Y chromosome sequencing...
Based on their mitochondrial genome and Y chromosome sequences, the team concluded that the individuals were likely descended from early European farmers who arrived in the region, mixing with local hunter-gatherer groups they encountered during this migration.
By comparing genome-wide SNP patterns in the samples with those in other ancient and modern European samples, the researchers were able to place the Iberian farmers in a genetic cluster with early farming groups in other parts of the continent.

parasar
09-08-2015, 04:02 PM
"6-year-old boy "Matojo" (ATP12-1420) from the Copper Age."
http://www.uu.se/en/media/news/article/?id=5072&area=2,5,10,16&typ=artikel&lang=en

"Matojo I2a2a2-S9403" https://genetiker.wordpress.com/2015/09/08/y-snp-calls-from-copper-and-bronze-age-spain/

ArmandoR1b
09-08-2015, 04:03 PM
We should know soon, since both Y and mtDNA apparently informed the paper's conclusions.
https://www.genomeweb.com/sequencing-technology/ancient-dna-study-suggests-basques-descended-early-iberian-farmers

For mtDNA the files don't need to be as large but for Y-DNA they do need to be sufficiently large.

Krefter
09-08-2015, 04:06 PM
That is inconsistent with R1.
The consistent reads would be:
R1b1-L389-P297-FGC46/Y97
R1b1-L389-P297-M269-PF6518

Though I have thought R2 could be a possibility too.
"trace amounts among Europeans - Portugal, Spain, Russia/Bashkort, Italy, Ossetia"
http://www.anthrogenica.com/showthread.php?5179-In-what-archealogical-cltures-wll-the-ancestors-of-R1a-L657-and-R1a-Tarim-be-found/page2&p=102855#post102855

He got a call in 1 R1 SNP and was positive, 1 R1b1a2 SNP and was positive, and 1 R1b1a2 or R1b1a2a SNP and was positive. He was tested for 1 R2 SNP and was positive.

ArmandoR1b
09-08-2015, 04:07 PM
"6-year-old boy "Matojo" (ATP12-1420) from the Copper Age."
http://www.uu.se/en/media/news/article/?id=5072&area=2,5,10,16&typ=artikel&lang=en


That page provides the range of dates for the specimens also


From these individuals who lived 3,500-5,500 years ago,

ADW_1981
09-08-2015, 04:19 PM
I haven't been following all the latest papers, but I would expect Copper/Bronze and the sudden appearance of Bell Beaker in Iberia to coincide with R1b-M269 and potentially I2-M223 no? These are the exact same two groups we saw in Yamnaya. Nothing from these results indicates that these were lineages introduced from Neolithic Farmers.

parasar
09-08-2015, 04:21 PM
I haven't been following all the latest papers, but I would expect Copper/Bronze and the sudden appearance of Bell Beaker in Iberia to coincide with R1b-M269 and potentially I2-M223 no? These are the exact same two groups we saw in Yamnaya. Nothing from these results indicates that these were lineages introduced from Neolithic Farmers.

My read of secondary sources is that the samples show no Yamna input.
They are the Els Trocs type with more La Brana type influence.

ADW_1981
09-08-2015, 04:22 PM
My read of secondary sources is that the samples show no Yamana input.

That's certainly possible, has nothing do with the origins of the YDNA. We saw some Central European Bell Beaker have little to no Yamnaya as well. We also know that hunter-gatherers after a couple of generations looked exactly like farmers.

parasar
09-08-2015, 04:27 PM
That's certainly possible, has nothing do with the origins of the YDNA. We saw some Central European Bell Beaker have little to no Yamnaya as well. We also know that hunter-gatherers after a couple of generations looked exactly like farmers.

I doubt it as they used Y to make a early European farmer connection.
I would go with the V88 or M479 lines, but would not be surprised by M269.

J Man
09-08-2015, 04:28 PM
How old is ATP3? Is this the same sample? -13,910* C,C http://mbe.oxfordjournals.org/content/early/2014/01/20/molbev.msu049.full.pdf
If these were early farmers, ie, only influenced by hunter-gathers, but not by later 5000ybp farmers, does this mean that either the early farmers or hunter-gathers (this looks unlikely) had M269?

Aren't they all from the Copper and Bronze Ages like the study says?...M269 makes perfect sense since these samples are from the Copper and Bronze Ages.

parasar
09-08-2015, 04:31 PM
Aren't they all from the Copper and Bronze Ages like the study says?...M269 makes perfect sense since these samples are from the Copper and Bronze Ages.

I disagree. M269 would be big news if it were to be found in a 5500 year old specimen showing no steppe input.

J Man
09-08-2015, 04:36 PM
I disagree. M269 would be big news if it were to be found in a 5500 year old specimen showing no steppe input.

Well either they are wrong about these individuals having no steppe input or these individuals were assimilated into Neolithic like societies and their steppe like ancestry has been diluted enough so as to not show up in an autosomal analysis.

jeanL
09-08-2015, 04:37 PM
That's certainly possible, has nothing do with the origins of the YDNA. We saw some Central European Bell Beaker have little to no Yamnaya as well. We also know that hunter-gatherers after a couple of generations looked exactly like farmers.

That's not quite the case, because even the most Iberian-like Central European Beaker sample that is R1b-L51 doesn't plot with Basques but with other Spaniards and is indeed east of Basques, suggesting that while this sample did indeed have less Yamnaya influence than other Central European beakers it still had Spanish levels of Yamnaya influence and had more than Basques. Therefore the presence of R1b-M269 in any sample pre-3000 BC an absence of the Steppe component will definitely call into question the association of R1b-M269 and the steppe component at least in Spain.

ADW_1981
09-08-2015, 04:43 PM
If this sample is pre-3000 BC (which would make it Iberian farmer rather than Bell Beaker), and if indeed the 1 call of M269 is accurate. I'm going to wait and see before drawing any conclusion. If by some chance M269 is found in an Iberian farmer, it would certainly indicate the "out of Iberia" farmers were tremendously more successful than the LBK ones. I'm also curious why all the Neolithic data to this point from Iberia has indicated the spread of G2.

R.Rocca
09-08-2015, 04:55 PM
My read of secondary sources is that the samples show no Yamna input.
They are the Els Trocs type with more La Brana type influence.

We'll have to wait and see...if they only compared the Portalon samples to farmers and western hunter-gatherers, then they would not be mentioning anything to the east.

ArmandoR1b
09-08-2015, 05:02 PM
SAMEA3477467 ATP3 only has 81 MB of coverage which is extremely poor. The ONLY M269 SNP that Genetiker was able to find was PF6518 which is found in many other haplogroups. Please do a search of it at http://www.yfull.com/search-snp-in-tree/ That same specimen also has calls for SNPs belonging to other haplogroups yet Genetiker only pointed out PF6518 which lead him to M269. That's being very careless.

Here is the result of the search of PF6518 at YFull.

− PF6518 G-FGC5672
This position for SNP is not in the YTree
− PF6518 J-CTS130
This position for SNP is not in the YTree
− PF6518 E-CTS1622
This position for SNP is not in the YTree
− PF6518 C-V20*
This position for SNP is not in the YTree
− PF6518 C1a1a1
This position for SNP is not in the YTree
− PF6518 R-M269
− PF6518 N-Y4374
This position for SNP is not in the YTree

jeanL
09-08-2015, 05:11 PM
The authors did not assign a haplogroup to ATP3 however it is indeed pre-3000 BC see here:

5846

Ohh yeah the study is out BTW!

alan
09-08-2015, 05:16 PM
There is the unknown origin of the pre-beaker Iberian copper age c. 3100BC-2800BC to take into account too (forts like Zambujal, Leciea, Villa Nova de Sao Pedro). They are often claimed as local evolution from farmers but that doesnt seem very likely given the arrival of copper and novel developed fortification ideas. I think rather like post-beaker El Argar which they finally IDed as coming from the east Med when they found evidence at La Bastida, the pre-beaker Iberian copper age origin point just has not been IDed yet. It too superficially looks like to me like it spread east to west along the Med. to Iberia but I am not sure from where. For it to include M269 though would be surprising because there are no intermediate points of M269 derivatives anywhere west of eastern Europe in the period 3000-2800BC.

If it was pre-3100BC then we are talking late Neolithic, not early copper age in normal terminology and that would be a huge surprise if M269 turned up before metals did.

parasar
09-08-2015, 05:16 PM
The authors did not assign a haplogroup to ATP3 however it is indeed pre-3000 BC see here:

5846

Ohh yeah the study is out BTW!

Wow Y-H2 again.

alan
09-08-2015, 05:17 PM
SAMEA3477467 ATP3 only has 81 MB of coverage which is extremely poor. The ONLY M269 SNP that Genetiker was able to find was PF6518 which is found in many other haplogroups. Please do a search of it at http://www.yfull.com/search-snp-in-tree/ That same specimen also has calls for SNPs belonging to other haplogroups yet Genetiker only pointed out PF6518 which lead him to M269. That's being very careless.

Here is the result of the search of PF6518 at YFull.

− PF6518 G-FGC5672
This position for SNP is not in the YTree
− PF6518 J-CTS130
This position for SNP is not in the YTree
− PF6518 E-CTS1622
This position for SNP is not in the YTree
− PF6518 C-V20*
This position for SNP is not in the YTree
− PF6518 C1a1a1
This position for SNP is not in the YTree
− PF6518 R-M269
− PF6518 N-Y4374
This position for SNP is not in the YTree

hrfhoiergjwgrkw[r

genetiker
09-08-2015, 05:20 PM
If it was pre-3100BC then we are talking late Neolithic, not early copper age in normal terminology and that would be a huge surprise if M269 turned up before metals did.

A huge surprise to you and to so many like you. Not a surprise to me.

This confirms everything I've been saying for over a year now, and what I've been called a "kook" and much worse for saying.

ArmandoR1b
09-08-2015, 05:21 PM
The authors did not assign a haplogroup to ATP3 however it is indeed pre-3000 BC see here:

5846

Ohh yeah the study is out BTW!

No Y-DNA haplogroup because the coverage was too low as I have stated before. I hope people learn too look at the file sizes from now on too.

genetiker
09-08-2015, 05:22 PM
SAMEA3477467 ATP3 only has 81 MB of coverage which is extremely poor. The ONLY M269 SNP that Genetiker was able to find was PF6518 which is found in many other haplogroups. Please do a search of it at http://www.yfull.com/search-snp-in-tree/ That same specimen also has calls for SNPs belonging to other haplogroups yet Genetiker only pointed out PF6518 which lead him to M269. That's being very careless.

Here is the result of the search of PF6518 at YFull.

− PF6518 G-FGC5672
This position for SNP is not in the YTree
− PF6518 J-CTS130
This position for SNP is not in the YTree
− PF6518 E-CTS1622
This position for SNP is not in the YTree
− PF6518 C-V20*
This position for SNP is not in the YTree
− PF6518 C1a1a1
This position for SNP is not in the YTree
− PF6518 R-M269
− PF6518 N-Y4374
This position for SNP is not in the YTree

Did you even look at the calls? He can't belong to any of those other haplogroups.

ArmandoR1b
09-08-2015, 05:22 PM
A huge surprise to you and to so many like you. Not a surprise to me.

This confirms everything I've been saying for over a year now, and what I've been called a "kook" and much worse for saying.

Why did you post results for a sample that has too low coverage to be able to reliably tell which haplogroup he belongs too?

genetiker
09-08-2015, 05:25 PM
Why did you post results for a sample that has too low coverage to be able to reliably tell which haplogroup he belongs too?

The calls show exactly which haplogroup he belonged to. R1b-M269.

ArmandoR1b
09-08-2015, 05:26 PM
The calls show exactly which haplogroup he belonged to. R1b-M269.

So you can't accept that you are wrong. Got it.

parasar
09-08-2015, 05:27 PM
Careless? Agenda more like
Low certainty no doubt, but of all the possibilities based on positive calls IMO M269 is the most likely.

K-CTS9278/PF5501/M2693
R1-M748/YSC0000207
R1b1-L389-P297-FGC46/Y97
R1b1-L389-P297-M269-PF6518

ArmandoR1b
09-08-2015, 05:31 PM
Low certainty no doubt, but of all the possibilities based on positive calls IMO M269 is the most likely.

K-CTS9278/PF5501/M2693
R1-M748/YSC0000207
R1b1-L389-P297-FGC46/Y97
R1b1-L389-P297-M269-PF6518

So now it is about faith.

parasar
09-08-2015, 05:36 PM
So now it is about faith.

No it's about likelihood. As genetiker mentioned none of the other possibilities you listed is a better fit.

alan
09-08-2015, 05:40 PM
Lets focus on what we do have:

The Ia2a guy is earlier than the earliest beaker date (c. 2800BC) according to recent reviews. So he is a pre-beaker copper age Iberian.

In fact the only guy on that table who falls within a beaker time period is the H2 guy. well at least much of his date range overlaps the earlier beaker period. There are no other beaker era males on this table.

alan
09-08-2015, 05:45 PM
Its a very disappointing report from a yDNA point of view. One H2 guy falls into the earlier beaker period although I am not clear if he is a beaker person. No other males of the beaker era were even tested.

alan
09-08-2015, 05:52 PM
The only mtDNA we have from this study which falls within the beaker period of Iberia is the beaker male (guy with H2 yDNA) who is mtDNA U5b3 and a female who is U5a1c. However the female is very late in the beaker phase so its possible she is not beaker. Anyone know anything about those mtDNA lines?

ADW_1981
09-08-2015, 06:01 PM
The two with reliable Y results fit within the other Neolithic results we've seen from YDNA in Iberia. This is not the first time I2-M223 has popped up and H2 I believe is the old F* or F3 we see from other Neolithic sites in LBK.

parasar
09-08-2015, 06:02 PM
http://www.pnas.org/content/early/2015/09/02/1509851112.full.pdf
http://www.pnas.org/content/suppl/2015/09/02/1509851112.DCSupplemental/pnas.201509851SI.pdf
http://www.pnas.org/content/suppl/2015/09/02/1509851112.DCSupplemental/pnas.1509851112.sapp.pdf

ATP2 displayed the derived allele for nine Y chromosome markers (Table S5); with all of the
markers providing phylogenetic support for ATP2 belonging to haplogroup H2. These
markers included: L985, L1013 and L1053 (A1); M235, P159 and P187 (F); L279, L281 and
P96 (H2). Previously labeled haplogroup F3, H2 was recently redefined on the basis of an
overlap between the datasets of [64] and [65] [63]. It was found that the two haplogroups, HM69
and F3-M282, shared a root defined by the marker M3035. While only a few H2
individuals have ever been found, the haplogroup appears to have a west Eurasian
distribution; with a low level Middle Eastern presence in modern-day Iran, Turkey, Bahrain,
Kuwait and Qatar (Family Tree DNA, [66]), as well as minor occurrences in modern-day
England, France, Sardinia, Sweden and the Netherlands (Family Tree DNA, [64,65,67]). H2
also seems to occur at low frequencies in Neolithic samples [68].

ArmandoR1b
09-08-2015, 06:06 PM
No it's about likelihood. As genetiker mentioned none of the other possibilities you listed is a better fit.

You can't consider better fits when there are so many no calls and such a thing as back mutations and recurrent SNPs and there aren't any calls for anything that is phylogenetically equivalent to P297 except for FGC46/Y97 and PF6518 is found in many other haplogroups. The specimen would need to have a lot other SNPs phylogenetically equivalent to P297 for the subclade to be reliably determined as being M269. Without that it is just conjecture, assumptions, or faith.

parasar
09-08-2015, 06:16 PM
46% migration edge from Motala12 line to MA1.
"Fig. 2. Admixture among ancient groups based on genome sequence data. (A) Admixture graph with four migration edges for the individual with the
highest sequencing coverage for each geographic site, region, or time period. To improve clarity, branch lengths are not drawn to scale and represent only
the hierarchical clustering (see SI Appendix, Fig. S10 for the topology drawn to scale)"

Humanist
09-08-2015, 06:19 PM
http://www.pnas.org/content/early/2015/09/02/1509851112.full.pdf
http://www.pnas.org/content/suppl/2015/09/02/1509851112.DCSupplemental/pnas.201509851SI.pdf
http://www.pnas.org/content/suppl/2015/09/02/1509851112.DCSupplemental/pnas.1509851112.sapp.pdf


ATP2 displayed the derived allele for nine Y chromosome markers (Table S5); with all of the
markers providing phylogenetic support for ATP2 belonging to haplogroup H2. These
markers included: L985, L1013 and L1053 (A1); M235, P159 and P187 (F); L279, L281 and
P96 (H2). Previously labeled haplogroup F3, H2 was recently redefined on the basis of an
overlap between the datasets of [64] and [65] [63]. It was found that the two haplogroups, HM69
and F3-M282, shared a root defined by the marker M3035. While only a few H2
individuals have ever been found, the haplogroup appears to have a west Eurasian
distribution; with a low level Middle Eastern presence in modern-day Iran, Turkey, Bahrain,
Kuwait and Qatar (Family Tree DNA, [66]), as well as minor occurrences in modern-day
England, France, Sardinia, Sweden and the Netherlands (Family Tree DNA, [64,65,67]). H2
also seems to occur at low frequencies in Neolithic samples [68].

Just a note that if they are referring to the members of the FTDNA F Project (https://www.familytreedna.com/public/F-YDNA/default.aspx?section=yresults), the sole Iranian representative is not an ethnic Iranian, but is rather an Assyrian (kit # N37056). Not that it is absent in ethnic Iranians necessarily. Since it is found in both Armenians and Assyrians, I would expect it to be found in neighboring groups as well.

parasar
09-08-2015, 06:21 PM
You can't consider better fits when there are so many no calls and such a thing as back mutations and recurrent SNPs and there aren't any calls for anything that is phylogenetically equivalent to P297 except for FGC46/Y97 and PF6518 is found in many other haplogroups. The specimen would need to have a lot other SNPs phylogenetically equivalent to P297 for the subclade to be reliably determined as being M269. Without that it is just conjecture, assumptions, or faith.

It is of low certainty/reliability, but it is not faith. If you have a better fitting haplogroup, please provide the evidence.

vettor
09-08-2015, 06:25 PM
Wow Y-H2 again.

Again!, where was it before?

H2 (ydna ) Gedrosian/south-asian?

Krefter
09-08-2015, 06:26 PM
SAMEA3477467 ATP3 only has 81 MB of coverage which is extremely poor. The ONLY M269 SNP that Genetiker was able to find was PF6518 which is found in many other haplogroups. Please do a search of it at http://www.yfull.com/search-snp-in-tree/ That same specimen also has calls for SNPs belonging to other haplogroups yet Genetiker only pointed out PF6518 which lead him to M269. That's being very careless.

Here is the result of the search of PF6518 at YFull.

− PF6518 G-FGC5672
This position for SNP is not in the YTree
− PF6518 J-CTS130
This position for SNP is not in the YTree
− PF6518 E-CTS1622
This position for SNP is not in the YTree
− PF6518 C-V20*
This position for SNP is not in the YTree
− PF6518 C1a1a1
This position for SNP is not in the YTree
− PF6518 R-M269
− PF6518 N-Y4374
This position for SNP is not in the YTree

Yeah, but he's negative for I, I2, J, G, T. He's even positive for K. Everything is in line for R1b1a2.

vettor
09-08-2015, 06:29 PM
The two with reliable Y results fit within the other Neolithic results we've seen from YDNA in Iberia. This is not the first time I2-M223 has popped up and H2 I believe is the old F* or F3 we see from other Neolithic sites in LBK.

F3 IIRC is now known as H1b ( ydna )

ArmandoR1b
09-08-2015, 06:33 PM
Yeah, but he's negative for I, I2, J, G, T. He's even positive for K. Everything is in line for R1b1a2.

How do you know he is negative for those? The coverage wasn't good enough for that.

Coldmountains
09-08-2015, 06:33 PM
Again!, where was it before?

H2 (ydna ) Gedrosian/south-asian?

Don't think that it has anything to do with Gedrosia or South Asia in this case. Y-DNA Haplogroup H is ultimately of West Asian origin and was probably brought to South Asia by a migration from West Asia in Neolithic times. It is also no coincidence that haplogroup G, distantly related to H, was so often found among Neolithic Farmers. But nevertheless it is quite fascinating that some H carriers moved so far west.

vettor
09-08-2015, 06:38 PM
The calls show exactly which haplogroup he belonged to. R1b-M269.

To get a clear picture on how your system works to detect markers, please run the known ydna from this paper so I may see these calls and no-calls. I am lost on how you decide what you have chosen.

ADW_1981
09-08-2015, 06:42 PM
http://www.pnas.org/content/early/2015/09/02/1509851112.full.pdf
http://www.pnas.org/content/suppl/2015/09/02/1509851112.DCSupplemental/pnas.201509851SI.pdf
http://www.pnas.org/content/suppl/2015/09/02/1509851112.DCSupplemental/pnas.1509851112.sapp.pdf

Not trying to make this personal, but I believe there is a "Boyd" cluster that is H2, and I know I have a South African cousin (probably Dutch) who is labeled F at 23andMe.

vettor
09-08-2015, 06:44 PM
Don't think that it has anything to do with Gedrosia or South Asia in this case. Y-DNA Haplogroup H is ultimately of West Asian origin and was probably brought to South Asia by a migration from West Asia in Neolithic times. It is also no coincidence that haplogroup G, distantly related to H, was so often found among Neolithic Farmers. But nevertheless it is quite fascinating that some H carriers moved so far west.

Agree, its fascinating that G2a, T1a of these central German Neolithic farmers with this H2 ( ydna ) could all have come from west-asian and could have travelled along the same path.
I see a northern iranian - northern anatolian route into Europe ( having drinkable water from caspian and black seas along the way )...........and also, since the paper also places these Neolithic "german" markers with the hungarian markers

Humanist
09-08-2015, 06:45 PM
F3 IIRC is now known as H1b ( ydna )

According to ISOGG (http://www.isogg.org/tree/ISOGG_HapgrpH.html), F3 is now H2:

http://i1096.photobucket.com/albums/g326/dok101/dok101089/F3_H2.jpg

vettor
09-08-2015, 06:52 PM
According to ISOGG (http://www.isogg.org/tree/ISOGG_HapgrpH.html), F3 is now H2:

http://i1096.photobucket.com/albums/g326/dok101/dok101089/F3_H2.jpg

yfull has H2 as a "dead line"
http://www.yfull.com/tree/H/

Bane
09-08-2015, 06:55 PM
As Genetiker published several days ago, Iron Age H1b from Bulgaria was eventually positive for E-Z1919: More Y-SNP calls from Iron and Bronze Age Bulgaria (https://genetiker.wordpress.com/2015/09/01/more-y-snp-calls-from-iron-and-bronze-age-bulgaria/). So can we assume that H2 for the Iberian sample is also not his terminal haplogroup?

Humanist
09-08-2015, 06:57 PM
yfull has H2 as a "dead line"
http://www.yfull.com/tree/H/

How can it be a "dead line" if there are men walking around today in Europe and Asia who are derived for M282?

parasar
09-08-2015, 07:01 PM
Again!, where was it before?

H2 (ydna ) Gedrosian/south-asian?
http://www.anthrogenica.com/showthread.php?3769-New-Leak-CWC-73-Yamna-modern-North-Euros-50-Yamna&p=68776&viewfull=1#post68776
"The sample close to Basal in Europe is confirmed H2 by the recent Haak paper on Yamna.

Near Basal (~0WHG, 0ANE):
STARCEVO_EN 5710-5550 cal BCE N1a1a1b Y-H2
"I0174 (Starcevo_EN) This individual was assigned to haplogroup H2 (L281:8353840T→G). Upstream haplogroup F was also supported (P142:7218079G→A, P145:8424089G→A, P138:14199284T→C, P316:16839641A→T, P14:17398598C→T, P159:18097251C→A). An individual bearing mutation P96 which also defines haplogroup H2 was found in the Netherlands21; while haplogroup H is rare in present-day Europeans, its discovery in I0174 suggests that it was present in Neolithic Europe.""

vettor
09-08-2015, 07:05 PM
How can it be a "dead line" if there are men walking around today in Europe and Asia who are derived for M282?

I am just stating what I see in yfull tree

jeanL
09-08-2015, 07:11 PM
It is of low certainty/reliability, but it is not faith. If you have a better fitting haplogroup, please provide the evidence.

Indeed the Vucedol R1b earlier sample was determined solely based on a single SNP, it couldn't even be tested for M269, yet you don't see anybody questioning its authenticity. smh!

ADW_1981
09-08-2015, 07:31 PM
Indeed the Vucedol R1b earlier sample was determined solely based on a single SNP, it couldn't even be tested for M269, yet you don't see anybody questioning its authenticity. smh!

It is different because it was reported in the actual paper by authentic researchers with credentials behind them.

J Man
09-08-2015, 07:32 PM
And no J2.

jeanL
09-08-2015, 07:39 PM
It is different because it was reported in the actual paper by authentic researchers with credentials behind them.

That's true! Perhaps we can get independent confirmation of the SNPs by a different person, that will definitely add some weight to it.

ArmandoR1b
09-08-2015, 07:41 PM
It is of low certainty/reliability, but it is not faith. If you have a better fitting haplogroup, please provide the evidence.
When there is insufficient data you can't have a best fit without jumping to conclusions.

Jean M
09-08-2015, 07:46 PM
Its a very disappointing report from a yDNA point of view. One H2 guy falls into the earlier beaker period although I am not clear if he is a beaker person.

The site is not Bell Beaker.

parasar
09-08-2015, 07:54 PM
When there is insufficient data you can't have a best fit without jumping to conclusions.

Perhaps if we consider it to be insufficient.
I think this result is consistent with a parallel line at Els Trocs and M269 at Vucedol. I will wait and see where smal and others put ATP3.

ArmandoR1b
09-08-2015, 08:03 PM
That's true! Perhaps we can get independent confirmation of the SNPs by a different person, that will definitely add some weight to it.
Do you have a PC that can run the BAM file SAMEA3477467 from http://www.ebi.ac.uk/ena/data/view/ERP010927 through the BAM analysis kit that can be downloaded from http://www.y-str.org/2014/04/bam-analysis-kit.html ?

ArmandoR1b
09-08-2015, 08:15 PM
Perhaps if we consider it to be insufficient.
I think this result is consistent with a parallel line at Els Trocs and M269 at Vucedol. I will wait and see where smal and others put ATP3.

The specimen also has calls for E1b1b1, I2, and J2. He could easily belong to any of those and I2 is the most likely since SAMEA3477474 ATP12 Matojo 3.3 GB was also.

jeanL
09-08-2015, 08:41 PM
The specimen also has calls for E1b1b1, I2, and J2. He could easily belong to any of those and I2 is the most likely since SAMEA3477474 ATP12 Matojo 3.3 GB was also.

He cannot easily belong to:

E1b1b1-V68-M78-V4057/L547/PF2166

when he has:

F-PF2756
F-FGC2054/Y1811
GHIJK-M3773/CTS12673

3 Positive F SNPs trump a single positive E SNP. But then again, this is assuming that the data provided by Genetiker is legit!

alan
09-08-2015, 08:58 PM
The site is not Bell Beaker.

yep - have read the paper now. Was previously just going by date.

alan
09-08-2015, 09:04 PM
Still find the paper not massively illuminating. Basque area was not a hotspot of development in the late Neolithic, early copper age, beaker phase, Early Bronze Age. Kind of off the beaten track. So, unusual levels of continuity from the Neolithic are to be expected. I understand the paper wasnt aiming at resolving the genetic history of Iberia in general of course. I hope people dont spend too much energy pointlessly trying to guess what a y line was when there is not enough data.

Krefter
09-08-2015, 09:05 PM
Can we move discussion about the Y DNA or R1b in El Portalon to another thread?

MitchellSince1893
09-08-2015, 09:15 PM
I am just stating what I see in yfull tree

Except for a few publicly available databases, I believe yfull only includes what has been submitted to it by individuals.

For example, compare the Yfull U152 tree to Richard Rocca's tree at the U152 project. Richard's is far more robust.

Jean M
09-08-2015, 09:24 PM
http://www.unz.com/gnxp/the-basque-culture-is-that-of-the-first-farmers/

Razib Khan weighs up the paper.


There’s a new paper in PNAS, Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. It is a nice complement to the earlier paper on an earlier Iberian Neolithic sample. These individuals all date to a later period, most ~5,000 years ago, and one ~3,500 years. Despite the media hype, the results of this paper were pretty much expected, and it’s the final nail in the coffin of the idea that the Basque language and culture are relics of Paleolithic Europe. Rather, it confirms the result that the Basque descend in large part from agriculturalists who brought the Neolithic revolution to Europe. The genetic result began to be clear as early as 2010, when PLOS BIOLOGY published A Predominantly Neolithic Origin for European Paternal Lineages. The interpretation of that paper was wrong in some of the specific detail. It is quite likely that the R1b haplogroup did not come with the first farmers, but that it was a later arrival. But, the authors were early in refuting the contention that the high frequency of this lineage among Basques was ipso facto evidence that it was a primal Paleolithic signature. In fact much of that work exhibited some circularity, with the premise that Basques were primal descendants of hunter-gatherers being the linchpin for archaeogenetic inferences which then came back around to pointing out that the intuited genetic distinctiveness of the Basques was further evidence of their uniqueness.

lgmayka
09-08-2015, 09:25 PM
yfull has H2 as a "dead line"
http://www.yfull.com/tree/H/
Someone in H2 (former F-M282) needs to order the Big Y.

genetiker
09-08-2015, 09:31 PM
I'm tired of my work being called into question by a bunch of people who are incapable of doing what I do themselves.

I'm tired of my work being criticized when it's superior to the work done by everybody else.

Anybody here contend that the results as I've presented them are wrong? Then download the data yourself and prove it. Otherwise, stop making baseless contentions.

And when somebody else shows that the calls are exactly as I've said they are, I expect an apology from all the naysayers, and recognition that this discovery of R1b-M269 in pre-Beaker Western Europe is mine and mine alone.

ArmandoR1b
09-08-2015, 09:38 PM
I'm tired of my work being called into question by a bunch of people who are incapable of doing what I do themselves.

I'm tired of my work being criticized when it's superior to the work done by everybody else.

Anybody here contend that the results as I've presented them are wrong? Then download the data yourself and prove it. Otherwise, stop making baseless contentions.

And when somebody else shows that the calls are exactly as I've said they are, I expect an apology from all the naysayers, and recognition that this discovery of R1b-M269 in pre-Beaker Western Europe is mine and mine alone.

Did you ever apologize to Felix?

Boreas
09-08-2015, 10:00 PM
Please keep personal queastions and comments via PM.

The PM-function is there for a reason.

Megalophias
09-08-2015, 10:10 PM
And when somebody else shows that the calls are exactly as I've said they are, I expect an apology from all the naysayers, and recognition that this discovery of R1b-M269 in pre-Beaker Western Europe is mine and mine alone.
Would you be so generous as to share credit with the guys who actually extracted, sequenced, and published the DNA? :rolleyes:

FTR I think you are probably right about the M269, though I don't think we can be certain with such a low coverage genome. But being the first guy to run it through a Y SNP finder gets you bragging rights, not all the credit.

alan
09-08-2015, 10:50 PM
Can we move discussion about the Y DNA or R1b in El Portalon to another thread?

Yeah the basic conclusions of the report and what the authors actually say is being lost on what is likely to always be an uncertain claim of R1b - contrary to the authors. If we really want to know when R1b entered Iberia the Basque country is a bad place to look IMO. Its not on the main path of changes seen 3000-2000BC in Iberia. Its actually one of the last places I would look in Iberia.

Gravetto-Danubian
09-08-2015, 10:50 PM
Genetiker

Congrats in advance if you're proven correct! . Despite some odd theories (homosexualism is a disease caused by eating bad Hay), you might be indeed gifted.

But your calls on the bulgarian samples are even more interesting. How did you discover that they are in fact males and not females - as the study authors argued ?

royking
09-08-2015, 10:52 PM
I'm tired of my work being called into question by a bunch of people who are incapable of doing what I do themselves.

I'm tired of my work being criticized when it's superior to the work done by everybody else.

Anybody here contend that the results as I've presented them are wrong? Then download the data yourself and prove it. Otherwise, stop making baseless contentions.

And when somebody else shows that the calls are exactly as I've said they are, I expect an apology from all the naysayers, and recognition that this discovery of R1b-M269 in pre-Beaker Western Europe is mine and mine alone.
Ted Kandell studied the BAM Files for ATP3 and finds multiple haplogroups derived all across the Y. Definitely no evidence that ATP3 is M269. Poor coverage!

alan
09-08-2015, 10:53 PM
Genetiker

Congrats in advance if you're proven correct! . Despite some odd theories (homosexualism is a disease caused by eating bad Hay), you might be indeed gifted.

But your calls on the bulgarian samples are even more interesting. How did you discover that they are in fact males and not females ?

LOL That is up there with an in-law who thinks its caused by tap water.

alan
09-08-2015, 11:04 PM
I long for the day when someone gets about 40 male ancient DNA samples across Iberia and puts the never-quite-dead 'undead' R1b from the west theory to bed. The slightest sniff of hope and all the usual suspects reanimate and come out of the woodwork across various forums. its the theory that just wont die. I dont know how on earth they expect M269 to have got to Iberia with the farmers without leaving any trail in the ancient DNA at points east between Iberia and Ukraine. We know the farmers got to Iberia largely from the Adriatic-Italy/S France/Iberia Cardial spread and that Cardial probably came from the Levant (not a part of SW Asia where L23 would have made its way into the steppes from). There is still an outside chance the spread of copper from the Balkans could have brought some M269 west (there were steppe elements in the Balkans from 4200BC some men of whom in theory could have mixed with the metalworkers) but every single ancient DNA datapoint from Ukraine to Iberia is against this.

parasar
09-08-2015, 11:21 PM
"The four Bulgarian teeth used in this study were obtained from four different excavations.

Sample P192-1 was found at the site of a pit sanctuary near Svilengrad, Bulgaria, excavated between 2004 and 2006.15*The pits are associated with the Thracian culture and date to the Early Iron Age (800–500 BC) based on pottery found in the pits. A total*of 67 ritual pits, including 16 pits containing human skeletons or parts of skeletons, were explored during the excavations. An upper wisdom tooth from an adult male was used for DNA analysis.

Sample T2G2 was found in a Thracian tumulus (burial mound) near the village of Stambolovo, Bulgaria. Two small tumuli dating to the Early Iron Age (850–700 BC) were excavated in 2008.16*A canine tooth from an inhumation burial of a child (c.12 years old) inside a dolium was used for DNA analysis.

Sample V2 was found in a flat cemetery dating to the Late Bronze Age (1500–1100 BC) near the village of Vratitsa, Bulgaria. Nine inhumation burials were excavated between 2003 and 2004.17*A molar from a juvenile male (age 16–17) was used for DNA analysis.

Sample K8 was found in the Yakimova Mogila Tumulus, which dates to the Iron Age (450–400 BC), near Krushare, Bulgaria. An aristocratic inhumation burial containing rich grave goods was excavated in 2008.18*A molar from one individual, probably male, was used for DNA analysis"

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824117/




Genetiker

Congrats in advance if you're proven correct! . Despite some odd theories (homosexualism is a disease caused by eating bad Hay), you might be indeed gifted.

But your calls on the bulgarian samples are even more interesting. How did you discover that they are in fact males and not females - as the study authors argued ?

jeanL
09-08-2015, 11:24 PM
Yeah the basic conclusions of the report and what the authors actually say is being lost on what is likely to always be an uncertain claim of R1b - contrary to the authors. If we really want to know when R1b entered Iberia the Basque country is a bad place to look IMO. Its not on the main path of changes seen 3000-2000BC in Iberia. Its actually one of the last places I would look in Iberia.

Atapuerca is not in the Basque Country (https://en.wikipedia.org/wiki/Atapuerca_Mountains), it is near it in Burgos, but still south of it.

Krefter
09-08-2015, 11:34 PM
Ted Kandell studied the BAM Files for ATP3 and finds multiple haplogroups derived all across the Y. Definitely no evidence that ATP3 is M269. Poor coverage!

Who's Ten Kendell? Can you give a link to his work?

Gravetto-Danubian
09-08-2015, 11:35 PM
I long for the day when someone gets about 40 male ancient DNA samples across Iberia and puts the never-quite-dead 'undead' R1b from the west theory to bed. The slightest sniff of hope and all the usual suspects reanimate and come out of the woodwork across various forums. its the theory that just wont die. I dont know how on earth they expect M269 to have got to Iberia with the farmers without leaving any trail in the ancient DNA at points east between Iberia and Ukraine. We know the farmers got to Iberia largely from the Adriatic-Italy/S France/Iberia Cardial spread and that Cardial probably came from the Levant (not a part of SW Asia where L23 would have made its way into the steppes from). There is still an outside chance the spread of copper from the Balkans could have brought some M269 west (there were steppe elements in the Balkans from 4200BC some men of whom in theory could have mixed with the metalworkers) but every single ancient DNA datapoint from Ukraine to Iberia is against this.

That was my original position, i.e. before 2014.- M269 spread as a late Neolithic/ copper age/ secondary products phenomenon from west asia, via Balkan sites like Varna, pre-Baden, etc.

Incidentally, Varna has been sampled and the paper on the way soon I hope.

Kopfjäger
09-08-2015, 11:53 PM
Who's Ten Kendell?

It's Ted Kandell (https://www.linkedin.com/pub/ted-kandell/5/b99/a3b)... *face-palms

Webb
09-09-2015, 12:04 AM
It's Ted Kandell (https://www.linkedin.com/pub/ted-kandell/5/b99/a3b)... *face-palms

That's funny!!

Moderator
09-09-2015, 12:21 AM
Folks, let us get away from talking about personalities and other trivialities and such and return to a discussion of the data. Thank you for the cooperation.

Krefter
09-09-2015, 12:26 AM
Watch tomorrow R1a-Z283 will pop up in Poland from 3500 BC, and R1a-Z93 in India from 3500 BC. When I saw the 3500 BC date for the R1b1a2 I'm totally shocked about the R1b1a2. Makes no sense at all.

EDITED

Gravetto-Danubian
09-09-2015, 12:32 AM
Watch tomorrow R1a-Z283 will pop up in Poland from 3500 BC, and R1a-Z93 in India from 3500 BC. When I saw the 3500 BC date from India. I'm totally shocked about the R1b1a2. Makes no sense at all.

I don;t understand your comment . Whats happening tomorrow?

pegasus
09-09-2015, 12:39 AM
Watch tomorrow R1a-Z283 will pop up in Poland from 3500 BC, and R1a-Z93 in India from 3500 BC. When I saw the 3500 BC date from India. I'm totally shocked about the R1b1a2. Makes no sense at all.

What paper published this Krefter??

Krefter
09-09-2015, 12:45 AM
I was speaking hypothetically. You guys speak English as your second language? Sorry, should have had that in mind.

Gravetto-Danubian
09-09-2015, 12:50 AM
Lol. Im a bit slow today

nuadha
09-09-2015, 12:58 AM
Watch tomorrow R1a-Z283 will pop up in Poland from 3500 BC, and R1a-Z93 in India from 3500 BC. When I saw the 3500 BC date from India. I'm totally shocked about the R1b1a2. Makes no sense at all.

Wait, are you convinced that the guy actually is m269? I thought is was a super sketchy inference at this point.

If he actually was m269 that would be a complete mindfuck.

R.Rocca
09-09-2015, 01:00 AM
I only had a chance to look at the positive calls Genetiker posted and they are valid. The sequence is of extremely poor quality. If I had a gun to my head and had to pick a haplogroup, I would say that it is more likely to be haplogroup R1b+ than any if the other groups proposed, but the authors were wise to not do that in the actual paper.

nuadha
09-09-2015, 01:05 AM
do you think someone should write to the authors?

Gravetto-Danubian
09-09-2015, 01:06 AM
I only had a chance to look at the positive calls Genetiker posted and they are valid. The sequence is of extremely poor quality. If I had a gun to my head and had to pick a haplogroup, I would say that it is more likely to be haplogroup R1b+ than any if the other groups proposed, but the authors were wise to not do that in the actual paper.

So it could actually be something like V88 again ?

pegasus
09-09-2015, 01:07 AM
I was speaking hypothetically. You guys speak English as your second language? Sorry, should have had that in mind.

Nope , English is my first language. I had a feeling you were being a bit sarcastic. Just wanted to confirm.

Generalissimo
09-09-2015, 01:10 AM
Watch tomorrow R1a-Z283 will pop up in Poland from 3500 BC, and R1a-Z93 in India from 3500 BC. When I saw the 3500 BC date from India. I'm totally shocked about the R1b1a2. Makes no sense at all.

What are you talking about?

parasar
09-09-2015, 01:11 AM
Wait, are you convinced that the guy actually is m269? I thought is was a super sketchy inference at this point.

If he actually was m269 that would be a complete mindfuck.

It is possible that some M269 moved west with V88 early, while the rest stayed back with M73.
That Kromsdorf M269 - wasn't that Bell Beaker?

ADW_1981
09-09-2015, 01:26 AM
It is possible that some M269 moved west with V88 early, while the rest stayed back with M73.
That Kromsdorf M269 - wasn't that Bell Beaker?

If it's legit I can think of another couple scenarios. The R1b-M269 (xL23) actually has a west Asian origin in this case, arriving with H2 and the Anatolian farmers, or alternatively was among the hunter gatherers of Iberia. We'll need more samples to define the picture further.

EDIT: L51+ has a plausible west Anatolian/Aegean origin. There is 1 sample at FTDNA From Greek Turkey, 1 Palestinian, and 2 distantly related Yemeni Arabs. These numbers may seem small, but are fairly numerous when you consider the rarity of L51 today. Unfortunately these L51+ folks a long dead and gone and the only way to prove their existance is by exhuming some bones and hoping to yield some YDNA. Remember that King Tut was R1b :D:D

nuadha
09-09-2015, 01:27 AM
It is possible that some M269 moved west with V88 early, while the rest stayed back with M73.
That Kromsdorf M269 - wasn't that Bell Beaker?

Of course there could always be stray groups wandering around but we don't actually see that much diversity in the adna samples so an m269 in pre beaker spain and an m269 in the steppe at the same time is unusual.

A 269 in pre beaker iberia would be very perplexing but it would not take away from solid argument of the eastern europe to western europe spread of "modern" m269. Any proposed path of m269 must include a branch going to the yamnaya. I think its ridiculous to argue m269 coming from western europe and making its way into the yamnaya. The population turnover is clear, yamnaya like groups moved from east to west. Megalithic like groups did not move to the steppe.

Still, m269 in pre beaker iberia would make me adjust some things.

I think i wasted too much time talking about this hypothetical.

Gravetto-Danubian
09-09-2015, 01:33 AM
It is possible that some M269 moved west with V88 early, while the rest stayed back with M73.
That Kromsdorf M269 - wasn't that Bell Beaker?

People are obviously skeptical of results . But if confirmed it must be as i said a few posts back- a west asian (?late) neolithic origin. You can forget about stray foragers. That's utter nonsense. Foragers don't "stray" 4000 miles west to iberia or central africa (in the case of V88).

Krefter
09-09-2015, 01:48 AM
What are you talking about?

Ha ha. Sorry that's a typo.

miiser
09-09-2015, 01:57 AM
Of course there could always be stray groups wandering around but we don't actually see that much diversity in the adna samples so an m269 in pre beaker spain and an m269 in the steppe at the same time is unusual.

A 269 in pre beaker iberia would be very perplexing but it would not take away from solid argument of the eastern europe to western europe spread of "modern" m269. Any proposed path of m269 must include a branch going to the yamnaya. I think its ridiculous to argue m269 coming from western europe and making its way into the yamnaya. The population turnover is clear, yamnaya like groups moved from east to west. Megalithic like groups did not move to the steppe.

Still, m269 in pre beaker iberia would make me adjust some things.

I think i wasted too much time talking about this hypothetical.

Honestly, it wouldn't surprise me to see M269 just about anywhere in Europe during this time. It seems like there is a tendency in these forums to think of haplogroups and cultures as uniform, homogeneous masses, migrating as rigid bodies from one place to another. I think it is true that, if you were to make a map, for example, of locations with 20% or greater M269 concentration, this would show a gradual move from east to west. But this sort of model is a gross simplification. A realistic model must take into consideration that there are thousands of individuals moving every which way, some as part of a gradual, identifiable mass migration, and others not. In many cases, the Brownian-diffusion like movement of a population may be much more significant than any structured movement in a particular direction. A realistic map of haplogroup movement would look much more like an ivy plant sending out tendrils in every direction (with some offshoots taking root and others not), rather than a big arrow moving slowly from east to west. I think people tend to forget this. Once a large population M269 mass is established in the east, you could easily have small groups or individuals creating far flung "colonies" within a relatively short time, far away from the main population center. Some of those may be associated with the archaeological appearance of their own culture in the new location. But many of them may leave no archaeological trace of their previous culture. Likewise, unless such colonies replace other populations of the region en masse, they may not leave a significant mark in the aDNA of later populations of the region.

Once any haplogroup has established a sizable population mass, it would not surprise me to find that haplogroup far away from its core within a relatively short time.

MitchellSince1893
09-09-2015, 03:07 AM
If M269 formed 12 to 15 thousand years ago (Yfull's dates http://www.yfull.com/tree/R-M269/); that's roughly 8000 years for some M269 descendants to migrate/travel from their origin to Iberia.

They could have traveled to Patagonia in that amount of time.

Generalissimo
09-09-2015, 03:26 AM
If 2/3 of the samples were R1b-M269 then that would be news.

But as things stand, with one iffy R1b-M269 and not even a single instance of L51 from prehistoric Iberia, all we can do is wait.

George
09-09-2015, 03:53 AM
These are good thoughts, Miiser. Take the interesting RISE 552 Yamna. The YDNA is of WHG origin, and not much if any farmer-type autosomal. It's way too early to become dogmatic about these matters.

Krefter
09-09-2015, 03:56 AM
These are good thoughts, Miiser. Take the interesting RISE 552 Yamna. The YDNA is of WHG origin, and not much if any farmer-type autosomal. It's way too early to become dogmatic about these matters.

Good point I forgot about that. The Yamnaya guy belonged to a deep I2a2 subclade shared by many today. Because I2a2 isn't popular today like R1b, people are more inclined to say I2a2 wandered off and ended up in Yamnaya somehow.

Gravetto-Danubian
09-09-2015, 04:12 AM
Honestly, it wouldn't surprise me to see M269 just about anywhere in Europe during this time. It seems like there is a tendency in these forums to think of haplogroups and cultures as uniform, homogeneous masses, migrating as rigid bodies from one place to another. I think it is true that, if you were to make a map, for example, of locations with 20% or greater M269 concentration, this would show a gradual move from east to west. But this sort of model is a gross simplification. A realistic model must take into consideration that there are thousands of individuals moving every which way, some as part of a gradual, identifiable mass migration, and others not. In many cases, the Brownian-diffusion like movement of a population may be much more significant than any structured movement in a particular direction. A realistic map of haplogroup movement would look much more like an ivy plant sending out tendrils in every direction (with some offshoots taking root and others not), rather than a big arrow moving slowly from east to west. I think people tend to forget this. Once a large population M269 mass is established in the east, you could easily have small groups or individuals creating far flung "colonies" within a relatively short time, far away from the main population center. Some of those may be associated with the archaeological appearance of their own culture in the new location. But many of them may leave no archaeological trace of their previous culture. Likewise, unless such colonies replace other populations of the region en masse, they may not leave a significant mark in the aDNA of later populations of the region.

Once any haplogroup has established a sizable population mass, it would not surprise me to find that haplogroup far away from its core within a relatively short time.

Yes very good points. But there is some method to the madness :)
Afterall peope don't "wander", or "get lost". Such termsoffer little explanation.

Migration and human mobility is planned and purposeful behaviour. I'm positive - whateve it is- some kind of order can be made for R1b- whether it's steppic or west-central asian. Migration was performed by specific groups of an overall population, and wasn't "in the thousands". Even the demic movements of agriculturalists was initially small, family based affair. Then further groups came, there was in situ multiplication, back-Migration, etc.

You also have to consider the people in question. Yes, palaeolithic foragers were capable of great tracks- but still piecemeal. But later mesolithic foragers were specially adapted to their ecological niches. Why would a fisher-forager from the Volga-Don "wander" to africa or iberia??

And we have to keep in mind repeat migrations, constant ebbs and tides. Because M 73 appears "native" on the steppe, it doesn't necessarily mean M269 was.

But I'm very much open minded. I had pretty much thrown away my west asian theory (for M269)for the steppe origin. But at the moment, I cannot look past central-west asia overall for M343.

nuadha
09-09-2015, 04:17 AM
A realistic model must take into consideration that there are thousands of individuals moving every which way, some as part of a gradual, identifiable mass migration, and others not. In many cases, the Brownian-diffusion like movement of a population may be much more significant than any structured movement in a particular direction. A realistic map of haplogroup movement would look much more like an ivy plant sending out tendrils in every direction (with some offshoots taking root and others not), rather than a big arrow moving slowly from east to west.

You'd be surprised. There is a strong amount of structure in genetic diversity and a lot of that is predicted by culture even after controlling for distance AND geological features. People quite frequently had a strong resistance of mixing culture and genetics. This allows for very different trajectories for different groups, such as farmers rapidly growing and spreading relatively unchanged. Not only that but there are definitely directional flows of people. During the neolithic it was from the south.

But over time all kinds of things happen in "random" ways (the pot mixes) as you say. At this time i still think its meaningful when you find, say, one blank lineage in 5 of the sampled lineages. Look at just how homogenous bell beaker, yamnaya, Corded ware, Hunter gatherers, and so forth have been.

I get the perspective you are coming from and you are correct. Im glad you said what you said but I just wanted to let you know that there is some legitimacy to the way others are thinking.

nuadha
09-09-2015, 04:24 AM
Once any haplogroup has established a sizable population mass, it would not surprise me to find that haplogroup far away from its core within a relatively short time.

For the haplogroup to be far flung. . . for sure. But to actually find it out of a just a few samples is not so likely. Whatever the relative populations sizes are we keep seeing so much regularity in an ancient cultures' dna.

Now that I think about it, isn't it pretty easy for a ydna lineage or a mtdna lineage to die out? Maybe thats why we don't see so many randomly assorted havens for a particular lineage. The lineage can make it far but its hard for a male only or female only lineage to make it. . . perhaps.

Heber
09-09-2015, 05:53 AM
Here is the response to my question on YFull re (ATP3) from Ted Kendall

The case for ATP3 being R1b1a2-M269 is as follows:
GHIJK-M3773/CTS12673 => K-CTS9278/PF5501/M2693 => R1-M748/YSC0000207 => R1b1a-L389-P297:FGC46/Y97 => R1b1a2-M269:PF6518
PF6518 [Y:23,099,729 A>C] is a transversion, and it's not a C>T or G>A which could be the result of DNA damage. Therefore, this could be a case for some kind of R1b1a2-M269 being present in the Pre-Bell Beaker/Chalcolithic 5526-5372 ybp (calBP + 60 years):
http://open-genomes.org/genomes/El_Portalon/Y/El%20Portalon%20ATP3%20R1b1a2-PF6518+.png

..........


YFull has the tMRCA for R1b1a2-M269* at 6132 ybp, and R1b1a2a-L23 at 5908 ybp, (old enough for ATP3 at 5526-5372 ybp) but there are 42 samples with *no* SNPs below L23 listed. (Is this correct, or are these just new / unpaid for samples that haven't been analyzed or reported yet?)
R-P312, which is typical of Western Europe has a tMRCA of only 4600 ybp, so it would be ruled out, and RISE98 from the Battle Axe/ Nordic Late Neolithic Culture in Sweden who is R-U106* was dated to 4285-4042 ybp.
It doesn't seem to be likely that R-U106 originated in Iberia in the Neolthic and migrated to Sweden to become part of the Battle Axe Culture, and R-U152 which was found in the Bell Beaker Culture in Germany at 4500 ybp is also too young.
If ATP3 is in fact some kind of R1b1a2-M269*, it's likely in one of the early non-R1b1a2a2-Z2103 branches, like we find in the Yamnaya Culture which arose shortly afterward, around 5300 ybp.

http://www.yfull.com/tree-more/R-M269/

Anabasis
09-09-2015, 06:21 AM
Here is the response to my question on YFull re (ATP3) from Ted Kendall

The case for ATP3 being R1b1a2-M269 is as follows:
GHIJK-M3773/CTS12673 => K-CTS9278/PF5501/M2693 => R1-M748/YSC0000207 => R1b1a-L389-P297:FGC46/Y97 => R1b1a2-M269:PF6518
PF6518 [Y:23,099,729 A>C] is a transversion, and it's not a C>T or G>A which could be the result of DNA damage. Therefore, this could be a case for some kind of R1b1a2-M269 being present in the Pre-Bell Beaker/Chalcolithic 5526-5372 ybp (calBP + 60 years):
http://open-genomes.org/genomes/El_Portalon/Y/El%20Portalon%20ATP3%20R1b1a2-PF6518+.png

..........


YFull has the tMRCA for R1b1a2-M269* at 6132 ybp, and R1b1a2a-L23 at 5908 ybp, (old enough for ATP3 at 5526-5372 ybp) but there are 42 samples with *no* SNPs below L23 listed. (Is this correct, or are these just new / unpaid for samples that haven't been analyzed or reported yet?)
R-P312, which is typical of Western Europe has a tMRCA of only 4600 ybp, so it would be ruled out, and RISE98 from the Battle Axe/ Nordic Late Neolithic Culture in Sweden who is R-U106* was dated to 4285-4042 ybp.
It doesn't seem to be likely that R-U106 originated in Iberia in the Neolthic and migrated to Sweden to become part of the Battle Axe Culture, and R-U152 which was found in the Bell Beaker Culture in Germany at 4500 ybp is also too young.
If ATP3 is in fact some kind of R1b1a2-M269*, it's likely in one of the early non-R1b1a2a2-Z2103 branches, like we find in the Yamnaya Culture which arose shortly afterward, around 5300 ybp.

http://www.yfull.com/tree-more/R-M269/

A post worth 100 papel

alan
09-09-2015, 07:21 AM
If M269 formed 12 to 15 thousand years ago (Yfull's dates http://www.yfull.com/tree/R-M269/); that's roughly 8000 years for some M269 descendants to migrate/travel from their origin to Iberia.

They could have traveled to Patagonia in that amount of time.

I dont think hunters are a possibility for any spread of stray M269 guys into the west. Even if it originated 13000-10000BC that is still post-LGM and there is no archaeological cultural connection between the hunters of that period in Iberia and in south Russia. The hunters in Iberia at that time were Azilians - a sort of Magdallenian derived group. The hunters in south Russia were unconnected. Any Magdallenian impulses halted short of the Carpathians in central Europe (giving way to Epi-Gravettians) and in eastern Europe didnt extend as far south as Ukraine or south Russia. So its really hard to see how there could possibly be any shared M269 in both areas or one area giving it to the other. With a line close to M73 in Samara in 5000BC it seems pretty clear P297 is of eastern origin.

As for farmers bringing M269 to Iberia. Well it is chronologically possible for an M269xL23 individual to do it if he was somehow incorporated into the Cardial movement west in either the Levant starting point or first European landing point in the Balkans Adriatic coast. However, as the Cardial farmers were already in the Adriatic by 6300BC it is too early for L23 so we would have to be talking an M269xL23 dead end rather than anything ancestral to P312. You simply cant have L23 in south Russia and Iberia c. 3500BC and explain it by farmers or indeed by hunters.

IF there is a stray M269 guy in Iberia the earliest possibility that is chronologically (in both a genetic and archaeological sense) would be if they guy was M269xL23 and was a stray eastern hunter who had made it into SW Asia (perhaps pushed their in the Younger Dryas from the north) or the Adriatic Balkans c. 6300BC and gotten incorporated in Cardial and swept along the Med. to Iberia c. 5500BC. It seems unlikely but the V88 shows this kind of thing could happen. Curiously there is a small M269xL23 concentration in the west Balkans.

However the key point is that is its too early and by definition too upstream for L23 and so is pretty much a dead end in the west (if it was ever confirmed).

The only other possibility is that an M269 guy got into Iberia at the end of the Neolithic but this guy is too old by several centuries to even be linked to the pre-beaker copper age in Iberia. He lived at a time when copper working had spread to Italy but not yet to southern France or Iberia. So the copper worker angle wouldnt work either.

So there are many archaeological and genetic dating reasons for either doubting a tentative M269 ID or being fairly certain it would have had to have been an M269xL23 dead end not ancestral to the great L23 family of clades.

alan
09-09-2015, 08:21 AM
Yes very good points. But there is some method to the madness :)
Afterall peope don't "wander", or "get lost". Such termsoffer little explanation.

Migration and human mobility is planned and purposeful behaviour. I'm positive - whateve it is- some kind of order can be made for R1b- whether it's steppic or west-central asian. Migration was performed by specific groups of an overall population, and wasn't "in the thousands". Even the demic movements of agriculturalists was initially small, family based affair. Then further groups came, there was in situ multiplication, back-Migration, etc.

You also have to consider the people in question. Yes, palaeolithic foragers were capable of great tracks- but still piecemeal. But later mesolithic foragers were specially adapted to their ecological niches. Why would a fisher-forager from the Volga-Don "wander" to africa or iberia??

And we have to keep in mind repeat migrations, constant ebbs and tides. Because M 73 appears "native" on the steppe, it doesn't necessarily mean M269 was.

But I'm very much open minded. I had pretty much thrown away my west asian theory (for M269)for the steppe origin. But at the moment, I cannot look past central-west asia overall for M343.

The key limiting factor as to the M73 and M269 origins is their upstream shared node of P297 which is not usually dated before 12000BC and is therefore post-LGM. There is no possible hunter link between an Azilian hunter in Iberia and some ANE heavy EHG in south Russia in the period 12000-5000BC. The only possible way of linking the two areas is if stray eastern hunters got caught up in farming waves west and lost their autosomal identity in the process. I see pressure microblades as originating in Siberian hunters and commencing spreading into both Europe and the northern fringes of SW Asia c. 9500BC. This kind of technology had reached the Levantine coast about 6500BC. So it is possible in theory at least that farmer waves in the pottery period moving into Europe from the Levantine coast after 6500BC could have had stray eastern hunter lineages. This sketch I have made is how I would see the most likely explanation for the V88 Iberian farmer and I suppose if this was a genuine M269xL23 guy I would say the same explanation is likely.

NB- for what it is worth, I suspect P297 may turn out to have been located among hunters of Siberian origin who moved first to the east Caspian/Aral Sea area before appearing in either Europe or SW Asia.

Gravetto-Danubian
09-09-2015, 08:57 AM
The key limiting factor as to the M73 and M269 origins is their upstream shared node of P297 which is not usually dated before 12000BC and is therefore post-LGM. There is no possible hunter link between an Azilian hunter in Iberia and some ANE heavy EHG in south Russia in the period 12000-5000BC. The only possible way of linking the two areas is if stray eastern hunters got caught up in farming waves west and lost their autosomal identity in the process. I see pressure microblades as originating in Siberian hunters and commencing spreading into both Europe and the northern fringes of SW Asia c. 9500BC. This kind of technology had reached the Levantine coast about 6500BC. So it is possible in theory at least that farmer waves in the pottery period moving into Europe from the Levantine coast after 6500BC could have had stray eastern hunter lineages. This sketch I have made is how I would see the most likely explanation for the V88 Iberian farmer and I suppose if this was a genuine M269xL23 guy I would say the same explanation is likely.

NB- for what it is worth, I suspect P297 may turn out to have been located among hunters of Siberian origin who moved first to the east Caspian/Aral Sea area before appearing in either Europe or SW Asia.

Alan, I really don't know where R1b overall originated, although I guessed western Central Asia on the basis of modern phylogeny. You could be correct that its ultimate origin could be in Siberian hunter-gatherers, who then trickled south to central Asia via the Keltiminar culture, etc. But in reality, the peri-LGM in central Asia is a knowledge void, and Siberia itself was depopulated during the LGM, so there must have been a third source - perhaps the Altai as you often suggest (but for which we lack any sold settlement data dating to 22- 18 kya). So we really don't know.

But I don't think the 'stray EHG' -cum-Iberia forager theory works. Why ? Because we have R1b (in the way of V88) in Africa also. The most obvious conclusion is that 343 groups were in central Asia at least by the Neolithic, and then V88 expanded via west Asia to Iberia and Africa - with perhaps mobile goat-herders, and in Europe this was a minor component compared to F* , G2a, etc groups.

As for M269, Im still leaning toward a steppe diffusion point east. Indeed, this recent uproar about the supposedly pre-BB M269 is not even confirmed. But if it is with more studies, and more samples, then we will have to accept that M 269 also originated south of the Caucasus somewhere and expanded like a 'pincer movement' - one north to the steppe and one west to southern Europe. We also have to not fix / limit our possibilities on the dating from YFull. As clever as those chaps are, there are confidence intervals to consider. And obviously aDNA, always trumps.

NB: the entire complexity of two or several waves of M269 into Europe must also be entertained (an elder M269 * and younger L51 -derived). What exciting times !

Jean M
09-09-2015, 09:15 AM
Here is the response to my question on YFull re (ATP3) from Ted Kendall. The case for ATP3 being R1b1a2-M269 is as follows

Thank you for taking so much trouble Heber. It is perfectly possible, indeed in my view likely, that R1b1a2-M269 or Z2103 moved into Lower Danube/Thrace c. 4000 BC in the early movement from the steppe that David Anthony described in chapter 11 of The Horse, The Wheel and Language. Copper-working ceased in the Balkans around this time, and my theory is that some copper-workers fled the climate change to settle in Sardinia. Paolo Francalacci et al. 2013 showed R1b1a2 having sufficient Sardinian-specific SNPs to qualify for an arrival in the Late Neolithic. So it would not surprise me if R1b1a2 was among the groups which gradually moved westwards to take copper-working into northern Iberia, separately from the arsenic-copper-working linked to the Stelae people in southern Iberia.

I have a suspicion that archaic Sardinian and pre-Basque were not Neolithic languages exactly, but languages descended from Neolithic languages of the Balkans, brought by copper-workers to Sardinia and the Pyrenees. There is an odd, so far unexplained, common feature with PIE that could have been acquired by contact of just the type one might get if some PIE speakers fled the steppe into the Balkans and were absorbed by speakers of a common ancestor to archaic Sardinian and Basque.

However, we must not get too excited, because this result from El Portalón is too dubious to be acceptable, given the limited coverage of the Y-chromosome. I certainly won't add it to my online table, or built anything upon it in print. But we might get a solid R1b1a2-M269 from ancient DNA in Copper Age Sardinia or SW France one day, completely separate from Bell Beaker sites.

Gravetto-Danubian
09-09-2015, 09:53 AM
Thank you for taking so much trouble Heber. It is perfectly possible, indeed in my view likely, that R1b1a2-M269 or Z2103 moved into Lower Danube/Thrace c. 4000 BC in the early movement from the steppe that David Anthony described in chapter 11 of The Horse, The Wheel and Language. Copper-working ceased in the Balkans around this time, and my theory is that some copper-workers fled the climate change to settle in Sardinia. Paolo Francalacci et al. 2013 showed R1b1a2 having sufficient Sardinian-specific SNPs to qualify for an arrival in the Late Neolithic. So it would not surprise me if R1b1a2 was among the groups which gradually moved westwards to take copper-working into northern Iberia, separately from the arsenic-copper-working linked to the Stelae people in southern Iberia.

I have a suspicion that archaic Sardinian and pre-Basque were not Neolithic languages exactly, but languages descended from Neolithic languages of the Balkans, brought by copper-workers to Sardinia and the Pyrenees. There is an odd, so far unexplained, common feature with PIE that could have been acquired by contact of just the type one might get if some PIE speakers fled the steppe into the Balkans and were absorbed by speakers of a common ancestor to archaic Sardinian and Basque.

However, we must not get too excited, because this result from El Portalón is too dubious to be acceptable, given the limited coverage of the Y-chromosome. I certainly won't add it to my online table, or built anything upon it in print. But we might get a solid R1b1a2-M269 from ancient DNA in Copper Age Sardinia or SW France one day, completely separate from Bell Beaker sites.

Hi Jean. That early movement (c. 4000 BC) from the steppe to the Balkans which Anthony describes has been interpreted differently by experts from the very countries from which the material derives. Suvorovo is indeed an early movement to the Prut steppe, but its material culture seems impoverished, and if anything, Suvorovo groups were under patronage of Cucuteni-Tripolye chiefs than vice-versa. Whatever the case, its was an early, low density drift westward, and ultimately abortive.

The colonization of the North and NW Black Sea steppe otherwise only took off c. 34/ 3300 BC, with groups like Usatavo - an outgrowth from Cucuteni-Tripolye communities, and Cernavoda likewise from local Copper Age Bulgarian groups. The kurgan ritual wasn;t specific to groups from the Azov-Capsian region - in fact they appear to have borrowed it from neighbouring agricultural groups.

I guess only aDNA will solve this question, but at the moment I'm hedging my bets with Ivanova, Rassamakin and Mazura (who've actually seen the evidence first hand :) )

Jean M
09-09-2015, 10:11 AM
Hi Jean. That early movement (c. 4000 BC) from the steppe to the Balkans which Anthony describes is doubtable. Indeed, experts from the very countries from which the material derives suggest that Usatavo is an outgrowth from Cucuteni-Tripolye communities, and Suvorovo-Cernavoda likewise from local Copper Age Bulgarian groups.

Usatovo is later. I'm talking about what Anthony calls the Suvorovo-Novodanilovka complex. As he says:


The archaeology that documents this event emerged into the literature in small bits and pieces over the last fifty years, and it is still not widely known. The steppe culture involved in the migration has been called variously the Skelya culture, the Suvorovo culture, the Utkonsonovka group and the Novodanilovka culture.

I realise that there has been a bias among archaeologists from Bulgaria, as indeed from almost every nation in Europe, to prefer a local origin over incomers for everything they dig up. This anti-migrationism has dominated archaeology for decades. It has been fostered by research agendas focused within national boundaries. However David Anthony has no bias in favour of any particular nation in the region in which he has chosen to specialise. He has published on the cultures of "Old Europe" as well as those of the steppe. He is, to say the least, familiar with the archaeology. Sometimes it is easier for an outsider to see the big picture. ;)

Gravetto-Danubian
09-09-2015, 10:28 AM
Usatovo is later. I'm talking about what Anthony calls the Suvorovo-Novodanilovka complex. As he says:



I realise that there has been a bias among archaeologists from Bulgaria, as indeed from almost every nation in Europe, to prefer a local origin over incomers for everything they dig up. This anti-migrationism has dominated archaeology for decades. It has been fostered by research agendas focused within national boundaries. However David Anthony has no bias in favour of any particular nation in the region in which he has chosen to specialise. He has published on the cultures of "Old Europe" as well as those of the steppe. He is, to say the least, familiar with the archaeology. Sometimes it is easier for an outsider to see the big picture. ;)

That's true, sometimes an outsider perspective is useful, although I sometimes I wonder about how convincing Anthony's perspective is. Eg in Chapter 6 he says he prefers Telegin's sequence to Rassamakin (mnore recent and based on larger body of evidence) because he "feels" its more correct. Hardly compelling argumentation.:) And Mazura and Rassamakin are Ukrainian. I don't think they'd be biased against the interpretations of Gimbutas and her modern supporters because Sredni Stog is in Ukraine, afterall.


But I edited my comment because I realise Id made an error in chronology. You're correct - Suvorovo is earlier, is indeed accepted as Dnieperian origin - and despite its short-lividness and sparsity it might have sent an offshoot rocketing to central-western Europe. Anythign is possible. But Usatavo and Cernavoda are argued to be derived from Neolithic groups by Mazura, Ivanova and the like. Whatever the case, Im sure we'd all like to see some Eneolithic and Bronze Age aDNA from the Black Sea littoral -(and indeed the Atlantic littoral !) to settle this question.

Jean M
09-09-2015, 10:44 AM
Usatavo and Cernavoda is seen as derived from Neolithic groups.

As I understand it, Usatovo has been seen as an extension of Late Tripolye into the steppe, mixing with steppe people, whereas Anthony (The Horse, The Wheel and Language, p. 349) also sees it as a mixture, but one dominated (politically) by people of steppe origin. The steppe element is plain in kurgan burials, while the upland farmers adopted the steppe custom of inhumation in a cemetery, but did not erect kurgans. The difference between the two perspectives on Usatovo may seem subtle, but political power is likely to affect which Y-DNA haplogroups came to dominate and to be carried up the Dniester into Corded Ware.

Gravetto-Danubian
09-09-2015, 11:02 AM
As I understand it, Usatovo has been seen as an extension of Late Tripolye into the steppe, mixing with steppe people, whereas Anthony (The Horse, The Wheel and Language, p. 349) also sees it as a mixture, but one dominated (politically) by people of steppe origin. The steppe element is plain in kurgan burials, while the upland farmers adopted the steppe custom of inhumation in a cemetery, but did not erect kurgans. The difference between the two perspectives on Usatovo may seem subtle, but political power is likely to affect which Y-DNA haplogroups came to dominate and to be carried up the Dniester into Corded Ware.

Correct. But I question - is kurgan burial really steppe and flat burials that of farmers ? (ie was it that simple a dichotomy? ) The other aspect to consider is that early "Kurgans" certainly appear in Eneolithic steppe cultures in the way of stone cairns, and mounds. But then they appear to disappear for 400 years, then reappear with different elaborations. It is on this basis - and that of a rather sudden population growth on the steppe c. 3200 BC - that Rassamakin and Mazura argue for a colonization from the forest-steppe, esp C-T cultures. Also we should note that the great catalyst for this period (M4) was Majkop. In comparison, the Azov-Caspian steppe - even during the Yamnaya proper phase- was scantily populated and poorer compared to Majkop and even Usatavo. So I think, whatever happened c. 3000 BC to Hungary and the west beyond, it might have more to do with "Majkopians" than the commonly perceived Repin-Sredny Stog- Yamnaya (or however it went) sequence. In fact, Majkop could have be ancestral to Yamnaya and Afansievo, more or less

But Im also curious as to the possibility of earlier movements east c. 4000 BC - as you suggested. But I can't see it coming from the steppe. The golden age there hadn't begun , and it was still a demographic and political "backwater". But anythings possible .

Jean M
09-09-2015, 11:16 AM
But Im also curious as to the possibility of earlier movements east c. 4000 BC - as you suggested. But I can't see it coming from the steppe. The golden age there hadn't begun , and it was still a demographic and political "backwater".

Movements east? I think you mean west.

c. 4000 BC there was a climate change which seems to have forced migration, as well as the collapse of the Balkan cultures of "Old Europe". I have suggested in AJ that farmers fled north up the Danube to emerge as the Funnel Beaker Culture. Meanwhile, I suggest, some Balkan copper-workers fled to Sardinia, where there was copper. The Ozieri culture emerges there at this time. Movement into Italy and northern Iberia seems to be rather later and could have come via Sardinia or some other staging post. I really don't know. But the point is that these movements were not direct from the steppe, bringing IE. These were remnants of Old Europe, which happened to have absorbed some steppe people via Suvorovo-Novodanilovka, as I see it. Could have been just one man!

The R1b1a2 in Sardinia did not bring an IE language or large amounts of ANE. It was essentially part of a Late Neolithic movement with copper i.e. Balkan.

alan
09-09-2015, 11:39 AM
That's true, sometimes an outsider perspective is useful, although I sometimes I wonder about how convincing Anthony's perspective is. Eg in Chapter 6 he says he prefers Telegin's sequence to Rassamakin (mnore recent and based on larger body of evidence) because he "feels" its more correct. Hardly compelling argumentation.:) And Mazura and Rassamakin are Ukrainian. I don't think they'd be biased against the interpretations of Gimbutas and her modern supporters because Sredni Stog is in Ukraine, afterall.


But I edited my comment because I realise Id made an error in chronology. You're correct - Suvorovo is earlier, is indeed accepted as Dnieperian origin - and despite its short-lividness and sparsity it might have sent an offshoot rocketing to central-western Europe. Anythign is possible. But Usatavo and Cernavoda are argued to be derived from Neolithic groups by Mazura, Ivanova and the like. Whatever the case, Im sure we'd all like to see some Eneolithic and Bronze Age aDNA from the Black Sea littoral -(and indeed the Atlantic littoral !) to settle this question.

I really liked Rassamakin's stuff when I first read into it but it slowly dawned on me that a lot of his interpretations could be interpreted as being Ukraine friendly and somewhat allergic to Russia. I may be wrong but it slowly came to feel like he preferred interpretations that didnt involve Russia :0)

alan
09-09-2015, 11:50 AM
Movements east? I think you mean west.

c. 4000 BC there was a climate change which seems to have forced migration, as well as the collapse of the Balkan cultures of "Old Europe". I have suggested in AJ that farmers fled north up the Danube to emerge as the Funnel Beaker Culture. Meanwhile, I suggest, some Balkan copper-workers fled to Sardinia, where there was copper. The Ozieri culture emerges there at this time. Movement into Italy and northern Iberia seems to be rather later and could have come via Sardinia or some other staging post. I really don't know. But the point is that these movements were not direct from the steppe, bringing IE. These were remnants of Old Europe, which happened to have absorbed some steppe people via Suvorovo-Novodanilovka, as I see it. Could have been just one man!

The R1b1a2 in Sardinia did not bring an IE language or large amounts of ANE. It was essentially part of a Late Neolithic movement with copper i.e. Balkan.

I think that makes a lot of sense. After 4200BC give or take, there is always a chance that M269 was present in low numbers mixed in with Balkans locals. The scale of the Suvorovo thing seems really small but it would be surprising if they left no R1 people mixed in with the locals. So, I agree, in theory any displacement or movement from the Balkans after 4200BC could have included the odd R1 guy although my feeling is their impact on autosomal DNA was probably very small indeed. I also agree that linking copper working spreading west along the Alps and into the central Med to the Balkans collapse and its long term repercussions makes complete sense. There is a sort of cline in copper working from the Balkans then post-collapse westwards c. 4000-3000BC. The only issue I would have with this dubious possibility of one of the guys in this paper being M269 is that he seems to pre-date even the pre-beaker Villa Nova de Sao Pedro (if that is still used as a blanket term) copper age culture of Iberia (unless you count the period where there is the odd stray copper trinket) in which case he would have to be some sort of stray from around Italy.

bicicleur
09-09-2015, 12:12 PM
what is not clear to me, where these people in El Portalon neolithic or chalcolithic?
the authors of the paper mention 'Chalcolithic El Portalón individuals'
is this incipient copper working ?
are there similairties with early Iberian chalcolithic sites like Los Millares or Zambujal?
what about copper smithing and copper ore smelting facilities?

alan
09-09-2015, 12:36 PM
what is not clear to me, where these people in El Portalon neolithic or chalcolithic?
the authors of the paper mention 'Chalcolithic El Portalón individuals'
is this incipient copper working ?
are there similairties with early Iberian chalcolithic sites like Los Millares or Zambujal?
what about copper smithing and copper ore smelting facilities?

well the guy who is the focus of the shaky claims of being R1b is Neolithic - predates by many centuries the pre-beaker copper age culture seen at Zambujal etc which is normally seen as the start of the chalcolithic in Iberia. This is a major reason why I doubt it is really R1b and dont think it should be claimed if doubt exists. If the sample had dated to 3000BC, the pre-beaker Iberian ealry chalcolithic then it may have been a little more believable.

George
09-09-2015, 12:44 PM
As I understand it, Usatovo has been seen as an extension of Late Tripolye into the steppe, mixing with steppe people, whereas Anthony (The Horse, The Wheel and Language, p. 349) also sees it as a mixture, but one dominated (politically) by people of steppe origin. The steppe element is plain in kurgan burials, while the upland farmers adopted the steppe custom of inhumation in a cemetery, but did not erect kurgans. The difference between the two perspectives on Usatovo may seem subtle, but political power is likely to affect which Y-DNA haplogroups came to dominate and to be carried up the Dniester into Corded Ware.

A lot of questions will remain unanswered until there is proper aDNA (esp. Y DNA) analysis of the Usatovo and Vykhvatinsk burials. The one thing Mazura and Rassamakin tried to do (to my mind unsuccessfully though valiantly) is to try to explain (indirectly) the vexed question of the fate of the Trypilian civilization. It's a major issue and has not yet been properly addressed. The peripheral Late Trypilian groups (Dnister, the Gorodsk group, the Sofiivka group) are archaeologically well studied and their evolution clear enough. The big mystery remains with the central Trypilian complex, the "megalopolises" like Maijdanets et sim., huge concentrations of populations, which suddenly disappear into thin air... The argument that they somehow travelled east and turned into Yamnites just doesn't hold. The archaeology is thin to nonexistent. And the issue of their fate is distinct from the emergence of Usatovo and the Late Trypilian groups. The only thoughts I have are rather fantastic. Associated with their "renewal through fire" ideology... Could that have been remotely possible? It's not a very pleasant idea...

Silesian
09-09-2015, 01:36 PM
A lot of questions will remain unanswered until there is proper aDNA (esp. Y DNA) analysis of the Usatovo and Vykhvatinsk burials. The one thing Mazura and Rassamakin tried to do (to my mind unsuccessfully though valiantly) is to try to explain (indirectly) the vexed question of the fate of the Trypilian civilization. It's a major issue and has not yet been properly addressed. The peripheral Late Trypilian groups (Dnister, the Gorodsk group, the Sofiivka group) are archaeologically well studied and their evolution clear enough. The big mystery remains with the central Trypilian complex, the "megalopolises" like Maijdanets et sim., huge concentrations of populations, which suddenly disappear into thin air... The argument that they somehow travelled east and turned into Yamnites just doesn't hold. The archaeology is thin to nonexistent. And the issue of their fate is distinct from the emergence of Usatovo and the Late Trypilian groups. The only thoughts I have are rather fantastic. Associated with their "renewal through fire" ideology... Could that have been remotely possible? It's not a very pleasant idea...


Do you agree with the facts/evidence provided in the lecture(Rassamakin)[13min-20min]-Indo-European Dispersals and the Eurasian Steppe with J.P. Mallory?


https://www.youtube.com/watch?v=Z0HCs6PVnzI

Jean M
09-09-2015, 02:12 PM
A lot of questions will remain unanswered until there is proper aDNA (esp. Y DNA) analysis of the Usatovo and Vykhvatinsk burials. The one thing Mazura and Rassamakin tried to do (to my mind unsuccessfully though valiantly) is to try to explain (indirectly) the vexed question of the fate of the Trypilian civilization. It's a major issue and has not yet been properly addressed. The peripheral Late Trypilian groups (Dnister, the Gorodsk group, the Sofiivka group) are archaeologically well studied and their evolution clear enough. The big mystery remains with the central Trypilian complex, the "megalopolises" like Maijdanets et sim., huge concentrations of populations, which suddenly disappear into thin air...

These are the people that I suggest moved up the Danube to emerge as the Funnel Beaker culture.

George
09-09-2015, 02:21 PM
Do you agree with the facts/evidence provided in the lecture(Rassamakin)[13min-20min]-Indo-European Dispersals and the Eurasian Steppe with J.P. Mallory?


https://www.youtube.com/watch?v=Z0HCs6PVnzI

Thank you for this. I've listened to the first 20 minutes and must say that I fully agree with his scepticism about the Trypilia eastward expansion. (I'll listen to the rest later). I can only repeat like Spock "Live long and prosper" (to Mallory that is. Great investigator.)

George
09-09-2015, 02:23 PM
These are the people that I suggest moved up the Danube to emerge as the Funnel Beaker culture.

You mean the Rassamakin thesis, but in a different direction? Is it "Danube" or "Dnister" you have in mind?

Jean M
09-09-2015, 02:31 PM
You mean the Rassamakin thesis, but in a different direction? Is it "Danube" or "Dnister" you have in mind?

From AJ 2nd edn:


The TRB was once seen as the result of local foragers adopting animal husbandry and new technology from their neighbours. This idea has been overturned by studies of ancient DNA. The Funnel Beaker peoples mainly carried mtDNA haplogroups typical of early farmers. Evidently migration spread this new way of life.

Copper axes and luxury wares from the Hungary-Serbia region travelled over 1000 km (620 miles) to the Baltic shore in the early 4th millennium BC. Another link lies in the Funnel Beaker pottery itself. Its decorative patterns were picked out with a paste made of bone. This technique originated in the Carpathian Basin. So the TRB may have been the result of farmers fleeing stricken settlements in the Balkans and Carpathian Basin for the milder climate of Northern Europe in this era. Later innovations such as wheeled vehicles, the plough and wool spinning seem to have fed into Funnel Beaker from its advanced southern neighbour, the Late Cucuteni-Tripolye culture ...

Genome-wide comparisons show that a Funnel Beaker female from Sweden and contemporary farmers from Germany, despite being most closely related to early European farmers, had somewhat more hunter gatherer ancestry. The same is true of their probable source population in Hungary, and indeed farmers in Spain between 4000 and 3000 BC. It seems that as farmers extended their territory, they absorbed some of the foragers who were being pushed to the fringes and ultimately to the extinction of their way of life.

R.Rocca
09-09-2015, 03:04 PM
well the guy who is the focus of the shaky claims of being R1b is Neolithic - predates by many centuries the pre-beaker copper age culture seen at Zambujal etc which is normally seen as the start of the chalcolithic in Iberia. This is a major reason why I doubt it is really R1b and dont think it should be claimed if doubt exists. If the sample had dated to 3000BC, the pre-beaker Iberian ealry chalcolithic then it may have been a little more believable.

I0410 from Els Trocs was dated 5178-5066 BC and is solidly R1b1 and also a V88 equivalent, so there is no need to doubt some forms of R1b were already expanding during the Early Neolithic and also very far from the steppe. Even if the El Portalon sample is a valid R+ and its PF6518+ is valid within a R1b context, remember that the M269 branch is made up of three dozen or so SNPs that may have needed thousands of years to build up, with only one single male line successfully surviving. Also to keep in our memory banks, I0559 from Baalberge and dated 3645-3537 BC was classified by Haak as R* even though it may be the result of ancient DNA damage. That said, none of this says nothing about where L23+L51+ arose.

bicicleur
09-09-2015, 03:06 PM
well the guy who is the focus of the shaky claims of being R1b is Neolithic - predates by many centuries the pre-beaker copper age culture seen at Zambujal etc which is normally seen as the start of the chalcolithic in Iberia. This is a major reason why I doubt it is really R1b and dont think it should be claimed if doubt exists. If the sample had dated to 3000BC, the pre-beaker Iberian ealry chalcolithic then it may have been a little more believable.

Los Millares is certainly older then 3000 BC
the exact dates for the first construction of Los Millares are not known, and people may even have arrived prior to that
the Los Millares people may have been prospects attracted by some findings of alluvial copper in the area, either by themselves or by local indogenous farmers
later they would have started looking for copper ores and have build their copper smelting facilities inside the newly built Los Millares
first arrival at Los Millares area may well have been contemporray with this ATP3 individual

George
09-09-2015, 03:18 PM
From AJ 2nd edn:(cf. post 246)

There's very little specifically CT in TRB. So mass movement thereto is even less likely than to the east. This isn't really the thread to discuss the problem of hunterforager input. I think there's a bit more to them than just "gene donation". Let it be for the moment. Would I be wrong to think that the only TRB aYDNA identified so far is I2a1b1a (Esperstedt--- looks like an "Isles" type?).

parasar
09-09-2015, 03:32 PM
Ted Kandell studied the BAM Files for ATP3 and finds multiple haplogroups derived all across the Y. Definitely no evidence that ATP3 is M269. Poor coverage!




Here is the response to my question on YFull re (ATP3) from Ted Kendall

The case for ATP3 being R1b1a2-M269 is as follows:
GHIJK-M3773/CTS12673 => K-CTS9278/PF5501/M2693 => R1-M748/YSC0000207 => R1b1a-L389-P297:FGC46/Y97 => R1b1a2-M269:PF6518
PF6518 [Y:23,099,729 A>C] is a transversion, and it's not a C>T or G>A which could be the result of DNA damage. Therefore, this could be a case for some kind of R1b1a2-M269 being present in the Pre-Bell Beaker/Chalcolithic 5526-5372 ybp (calBP + 60 years):
http://open-genomes.org/genomes/El_Portalon/Y/El%20Portalon%20ATP3%20R1b1a2-PF6518+.png

..........


YFull has the tMRCA for R1b1a2-M269* at 6132 ybp, and R1b1a2a-L23 at 5908 ybp, (old enough for ATP3 at 5526-5372 ybp) but there are 42 samples with *no* SNPs below L23 listed. (Is this correct, or are these just new / unpaid for samples that haven't been analyzed or reported yet?)
R-P312, which is typical of Western Europe has a tMRCA of only 4600 ybp, so it would be ruled out, and RISE98 from the Battle Axe/ Nordic Late Neolithic Culture in Sweden who is R-U106* was dated to 4285-4042 ybp.
It doesn't seem to be likely that R-U106 originated in Iberia in the Neolthic and migrated to Sweden to become part of the Battle Axe Culture, and R-U152 which was found in the Bell Beaker Culture in Germany at 4500 ybp is also too young.
If ATP3 is in fact some kind of R1b1a2-M269*, it's likely in one of the early non-R1b1a2a2-Z2103 branches, like we find in the Yamnaya Culture which arose shortly afterward, around 5300 ybp.

http://www.yfull.com/tree-more/R-M269/

So apparently Ted Kendall now thinks that M269 is a possibility.

Assuming that to be the case we have the following:

1. R1b-M269 PF6518 in Iberia ~5500 ybp.
2. R1b-PF6376 in Iberia >7000ybp
3. Both L389 and V88 lines are present pre-Beaker in Iberia.
4. Both samples do not show any steppe influences.

While I'm still not buying Genetiker's Iberian refuge theory and consider a steppe origin likely for R1b overall, how do we reconcile the evidence, which has this nasty habit of coming in the way of theories!

We have very little time to play with since the time-frame of ATP3 is quite close to the time-frame of the birth of M269 itself.

What is the difference in the R1a samples we are seeing in Corded Ware and the R1b in Bell Beaker?

Quoting Richard A. Rocca:
http://www.anthrogenica.com/showthread.php?4255-Genetic-Drift-Sharing-Bell-Beaker-amp-WHG

Haak's figure S7.7b shows populations that share the most genetic drift with Bell_Beaker_LN (or more specifically, German Bell Beakers). In order of most sharing, they are:

Group 1:

1. HungaryGamba_HG (a.k.a KO1, Neolithic of hunter-gatherer ancestry, halpogroup I2a)
2. Loschbour (based on an 8,000 year-old hunter-gatherers from Loschbour, Luxembourg, haplogroup I2a)
3. Motala_HG (based on seven 8,000 year old hunter-gatherers from Motala in Sweden., 5 of 5 males haplogroup I2)
Note: Interestingly these first three are Western or Scandinavian Hunter Gatherer groups and not EHG. All are I2.

Group 2:

4. Alberstedt_LN (possibly of mixed Corded Ware/Bell Beaker ancestry as per Haak, 2459-2345 cal BCE)
5. Esperstedt_MN (dated to 3360-3086 cal BCE, haplogroup I2a1b1a)
6. Karsdorf_LN (possibly Corded Ware, radiocarbon dating pending)
7. BenzigerodeHeimburg_LN (possibly all Bell Beaker)
8. Corded_Ware_LN (haplogroup R1a)
9. SwedenSkoglund_NHG (haplogroup I2)
10. Karelia_HG (haplogroup R1a)
11. Halberstadt_LBA (haplogroup R1a)
12. Unetice_EBA (3 of 3 males haplogroup I2)
13. Samara_HG (haplogroup R1b1)
Note: The bulk of this group is made up of possible Bell Beaker mixes or later groups with Bell Beaker ancestry. However, the Esperstedt_MN sample is the lone Neolithic sample and of interest because it groups with Spain_MN (2 of 2 males haplogroup I2a). It is not until the 10th (Karelia_HG) and 13th (Samara_HG) spot that we get to EHG samples.

Group 3:

14. Spain_MN (3900-3600 BCE, 2 of 2 samples haplogroup I2a)
15. Spain_EN (5311-5066 cal BCE, 1 sample R1b1, the other F*
Note: This group is interesting because Bell_Beaker_LN shares more genetic drift with these two Spanish Neolithic populations than all other Central European Neolithic samples except for the previously mentioned Esperstedt_MN. Of further interest, both male Spain_MN samples also belong to haplogroup I2a. One Spain_EN sample is I2a, the other is R1b1* and while the third sample could only be assigned to F*, he is a relative of the R1b1* sample and enough of the usual hunter/farmer haplogroups have been ruled out (e.g. G, I1, I2, T), that he could also be R1b1.

After that you get a mix of Neolithic and modern populations. Way down the list we have the HungaryGamba_CA (Baden Culture) sample, which is is a typical EEF, finding it's closest likeness to another Balkan Neolithic group in Starcevo_EN. Another Copper Age Central European, Otzi the Iceman, also shares his most genetic drift with Starcevo_EN. Theoretically, a Yamnaya movement westward should produce a Yamnaya mix with a HungaryGamba_CA/Iceman/Starcevo type population. Instead, we have the following:

Figure S9.8b the modeling of Bell_Beaker_LN as a mixture of earlier populations...
24.8% Karelia_HG + 75.2% Spain_MN
49.5% Spain_MN + 50.5% Yamnaya

So, what does this all mean for R1b? While the appearance of Yamnaya ancestry across all of Europe still makes a movement of R1b-L51 & R1b-L11 from east to west during the Late Neolithic very likely, these German Bell Beaker samples seem heavily mixed with Western European Hunter-Gatherers. They shed some of their EHG, more so that their distant R1a Corded Ware cousins. Unlike the Corded Ware samples, the German Bell Beakers do have Western Mediterranean ancestry. Was this a mix with a Western European Megalithic population, perhaps mainly females belonging to mtDNA haplogroup H...perhaps they themselves the daughters of I2a males? Is genetic drift hinting at a P312+ Rhenish Bell Beaker or Iberian Bell Beaker re-expansion...or perhaps both? IMO, a clean and uniform east to west movement and growth is not backed by Haak's genetic drift nor admixture tests. Certainly both leading Bell Beaker expansion models (Iberian/Dutch) show expansions from Western Europe, not from the Danube. Of course we will only know for sure once we get ancient DNA from places like the Netherlands (Protruding Foot Beaker Culture), France (Seine-Oise-Marne culture), Italy (Remedello Culture) and across different periods of time, but we need to keep all options open, because one thing that the predominantly Z2103+ Haak results showed us, is that ancient DNA is full of surprises.

There clearly seems to a connection among Y-H2, I2, and R1b types and a WHG+EEF mix. While Richard feels that the German Beakers have shed their EHG, is it also possible that they gained the EHG after coming into contact with R1a1 types?