Tuesday, September 26, 2017

DNA - The Violet Volken? (Fregel et al, 2017)

Something curious is afoot.  New questions emerge from this paper.

I guess I've mis-understood the Ifri n'Amr o'Moussa cave site from the outset unless it's been re-dated, it seems that all of the human remains buried here (facing NS and EW) are dated to be Cardial Farmers more than likely, not associated with the Beaker materials of this cave.  If I understand correctly, no human remains in this cave can be attributed to the Beaker period.  These samples are called IAM after the excavation, and they look like a mixture of early farmers and native people.  

The second site of Kehf el Baroud is the site that raised my antennas.  These samples are called KEB and come from a white layer dated to around 3200-3000, right below the grey Beaker horizon.  This archaeological layer is associated with a pottery tradition that some have described as proto-Beaker, including (Daugas et al, 1989) or more often 'influences' from here can be seen on the later ceramic.

During this time, extensive trade is occurring between the Portuguese castillos, Southern Spain and nearby burial sites like Rouazi-Skhirat and El Kiffen. (also The Ivory Road) Now a genetic relationship and population movement can be demonstrated as well.  In fact, based on the mtdna profiles and comments in this draft, it looks something short of population turnover with people coming from Iberia at some point before the LN.

KEB is, to some degree, a combination of a previous Moroccan mix with a strong and distinctly European vein that is suggestive of a SW European expansion, and curiously they specifically mention this 'violet component' rise in Middle Neolithic Central Europe with Baalberge and Salzmunde, which they see as moving from SW Europe.  Another distinct part of those and Michelsberg was a spike in WHG ancestry emanating from the Paris Basin and probably further south, although there are 'steppic' or SE European elements as well .  See previous post.

IAM girl with millstone?  Moroccan Press

Remember that the results below are from only two Moroccan caves so it's definitely not the full picture, but interestingly haplogroup H is missing from the Mesolithic/Early Neolithic 'native' set. Keeping in mind it's only one cave, it still seems significant because it's there in modern times, among some Saharan and Atlas Berbers in spades.
If there were more bodies to test from the pre-Beaker and Bell Beaker period, it's likely that one or both could have some M269.  It's definitely there by the first millennium.  Canary Islander DNA from the first millennium.

"By 3,000 BCE, a European Neolithic expansion brought Mediterranean-like ancestry to the Maghreb, most likely from Iberia. Our analyses demonstrate that at least some of the European ancestry observed today in North Africa is related to prehistoric migrations, and local Berber populations were already admixed with Europeans before the Roman conquest. Furthermore, additional European/Iberian ancestry could have reached the Maghreb after KEB people; this scenario is supported by the presence of Iberian-like Bell-Beaker pottery in more recent stratigraphic layers of IAM and KEB caves."
And here something interesting
"At K=8, a new violet component is majoritarian in Iberian Neolithic_EN and most Europe_MNChL, splitting from the early farmers green component.  Europe_MNChL samples that posses 100% of the violet component include Early/Middle Neolithic and Chalcolithic sites from Iberia, Middle Neolithic sites from Germany (Baalberge and Salzmuende cultures) and a Chalcolithic site from Italy (Remedello culture) (Figure S7.4). This result could indicate an, at least partial, Iberian component in Middle Neolithic and Chalcolithic populations in Germany and Italy."
And the dating of Kehf el Baroud
"The human remains analyzed in this study were obtained from the white layer, whose
pottery remains are quite similar to Late Neolithic and Early Chalcolithic pottery from
other locations in Morocco, such as the two neighboring necropolis of Rouazi-Skhirat and El Kiffen, and from Spain and Portugal, primarily in Los Millares and Vila Nova de Sao Pedro. The dating of the white layer performed by De Wailly13, giving an age of about 3,200 BCE, has been disputed by most researchers. However, this date has been confirmed previously by thermoluminescence12 and by calibrated radiocarbon dating in this study (Table S1.1, Figure 1.4)."
I'm still puzzled by the presence of V88 in the Sahel.  I figured it'd be present among the Cardium/Impresso peoples, but that hasn't panned out so far.  Maybe it comes from Iberia with Beakers or MN Iberians?

"Background to Beakers" page 196

BTW, read the last four page of Background to Beakers beginning on page 196.  Pretty impressive.

Yussaef Bokpot previously did a translatable Arabic interview [here]

Neolithization of North Africa involved the migration of people from both the Levant and Europe

Rosa Fregel, Fernado L. Mendez, Youssef Bokbot, Dimas Martin-Socas, Maria D. Camalich-Massieu, Maria C. Avila-Arcos, Peter A. Underhill, Beth Shapiro, Genevieve L Wojcik, Morten Rasmussen, Andre E. R. Soares, Joshua Kapp, Alexandra Sockell, Francisco J. Rodriguez-Santos, Abdeslam Mikdad, Jonathan Santana, Aioze Trujillo-Mederos, Carlos D. Bustamante
Supplement 1
One of the greatest transitions in the human story was the change from hunter-gatherer to farmer. How farming traditions expanded from their birthplace in the Fertile Crescent has always been a matter of contention. Two models were proposed, one involving the movement of people and the other based on the transmission of ideas. Over the last decade, paleogenomics has been instrumental in settling long-disputed archaeological questions, including those surrounding the Neolithic revolution. Compared to the extensive genetic work done on Europe and the Near East, the Neolithic transition in North Africa, including the Maghreb, remains largely uncharacterized. Archaeological evidence suggests this process may have happened through an in situ development from Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. In fact, Neolithic pottery in North Africa strongly resembles that of European cultures like Cardial and Andalusian Early Neolithic, the southern-most early farmer culture from Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Andalusian Early Neolithic individuals. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, indicating long-term genetic continuity in the region. Among ancient populations, early Neolithic Moroccans share affinities with Levantine Natufian hunter-gatherers (~9,000 BCE) and Pre-Pottery Neolithic farmers (~6,500 BCE). Late Neolithic (~3,000 BCE) Moroccan remains, in comparison, share an Iberian component of a prominent European-wide demic expansion, supporting theories of trans-Gibraltar gene flow. Finally, the Andalusian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ~5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian intrusion into the Maghreb.


  1. My read of the data is that V88 has its source in a male dominated pastoralist group that makes its way from the Steppe to the Levant to the Nile. These proto-Chadic people marry Cushitic wives the encounter in what is now Upper Egypt or Sudan, and then migrate up the now dry Yellow Nile River bed and hop over the divide between the Nile Basin and the Lake Chad endoheric basin ca. 5200 BCE. I collect some of the evidence for that case at http://dispatchesfromturtleisland.blogspot.com/2014/03/the-holocene-climate-events-that-shaped.html Eventually, over the centuries, some V88 bleeds out via admixture with neighboring groups into nearby non-Chadic populations.

    1. There's no doubt in my mind that it originates somewhere in the vicinity of the Western or Northern Black Sea. I'm just curious as to what archaeological culture it is associated with and what direction it took. After that, everything you've said above I agree with.

    2. The strong corroboration from multiple lines of evidence of the 5200 BCE arrival at Lake Chad date and the requirement that they would have had to have been pastoralists for the duration of their long distance journey puts some pretty tight bounds on potential archaeological cultures at the place of origin. The first wave Neolithic reached Egypt around 7000 BCE (very early), but probably reached the Steppe somewhat later (the Horse, the Wheel and Language would be good to narrow the candidate cultures), so you've got many centuries less than an 1800 year window in a pretty specific geographic location among people who are not directly traceable to Anatolian Neolithic migrants but did pick up animal husbandry in that time frame.

      There aren't a lot of choices when it comes to direction of travel either. They either went to the east of the sea and over the mountains through Armenia or eastern Anatolia and then down into the Fertile Crescent, or they crossed the isthmus and straits to the west of the sea and travelled through western Anatolia. Either way, eventually they have to stroll down the Levantine Coast or along its foothills across the Sinai to Egypt (the route through Yemen isn't suitable with herds of cattle traveling along with you), then down the Nile and turn west at the White Nile until you reach its source and go over the low rise mountains between the source and Lake Chad.

      Along the Black Sea coast you can't start much further west than the Danube and you can't start much further east than the foothills of the Caucasus. Given that they are basal R1b and not basal R1a, they've pretty much got to be nowhere north of Ukraine. Given these pretty tight geographic boundaries, the less than 1800 years temporal window, the requirement that they be pastoralists, the requirement that the archaeological culture can't be dead large numbers of centuries before 5200 BCE, and the requirement that the not be EEF stock, the range of possibilities is pretty narrow. I'd also strongly favor cattle herders over sheep and goat herders, because it is pretty clear that the proto-Chadic people had cattle among the livestock that they were herding. Realistically, they probably had to be around at their point of departure sometime in the window of 6000 BCE to 5200 BCE.

      The time depth and probably language shift and their cultural ethnogenesis following their marriages to local women all make any effort to use linguistic, legendary or cultural cures to identify them probably futile. The trip also predates any written records of any kind by thousands of years and doesn't seem to have left any notable traces of V88 that persisted en route.

      As far as I'm concerned, a route the long way around the Mediterranean via the Straits of Gibraltar is basically unthinkable knowing that they interacted with Cushitic women en route and ended up at Lake Chad.

    3. From what I've seen of the V88 tree, I would also favor this Eastern origin. I guess it will just take ancient DNA from Saharan and Sudanese burial sites to pinpoint it to a at least one defined culture. It wouldn't surprise me if it expanded about the same time as M269 due to the way they both seem to have explosive characters.

    4. The culture they passed through in the Levant would have had to be Pottery Neolithic which was in the Fertile Crescent from 6400 BCE to 4500 BCE. The Ubaid culture would have been in Southern Mesopotamia and probably wouldn't have been encountered. Apparently, sheep and goats reach Egypt around 6000 BCE, so they would have had to have reached Egypt after 6000 BE. If they took a western route they might have encountered the fringes of the early Vinca culture of the Balkans (5700 BCE to 4500 BCE) but probably wouldn't belong to it. The Vinca did have cattle, however.

      The Cucuteni–Trypillia culture ca. 5200 BCE to 3500 BCE is in the right place (centered on Moldova), but timing-wise would more likely be the culture immediately after the proto-Chadic migrants left. They too had cattle.

      The Starčevo culture, sometimes included within a larger grouping known as the Starčevo–Kőrös–Criş culture, is at about the right time (6200 BCE to 4500 BCE) and in about the right place, the north banks of the Danube, but they were a settled farming community and would be pushing the boundaries of being too far west as a starting point. So, probably a culture contemporaneous with them, but further east and without farming.

      Linear pottery also involves farmers and is too far west and north.

      Now, the Bug-Dniester culture was the archaeological culture that developed in the chernozem region of Moldavia and Ukraine around the Dniester and Southern Bug rivers flourished from 6300 BCE to 5500 BCE, which is just about right in terms of timing and location. They adopted cattle-breeding from the Cris people to the west ca. 5800 BCE to 5700 BCE, but were only primitive and recent farmers who weren't very admixed with the Cris, so this culture would be a very attractive candidate as a source for V88 people in Africa.

      The Dnieper–Donets culture comes to late (flourishing ca. 5000 BCE to 4200 BCE), even though they are in pretty close to the right place and they were still transitioning out of a hunter-gatherer period at that point. But, while this culture is ruled out, the fact that cattle herding hadn't reached as far east as the Dnieper by 5000 BCE and that cattle herding was a technology moving from west to east at that point in time, pretty much narrows our geographic range to someplace west of the Dnieper and east of the Danube.

      The bottom line from a pretty straightforward analysis is that the Bug-Dniester culture is pretty much far and away the most plausible candidate for a source of V88 people in Africa in terms of the nature of their animal husbandry, the timing, the location relative to hunter-gatherer and farming cultures of the time, and the fact that they have a location which would be plausible for R1b-V88 people to be located at that point in time.

      Assuming that the Bug-Dniester culture is the solution, I think the route is pretty clear as well. A route that goes generally southwest from the Bug-Dniester region through Moldova, through Romania, through Bulgaria, through Western and Central Anatolia, through Syria and Lebanon and Israel to Cairo, Egypt and the south along the Nile is really the only route that makes sense for them. (Obviously, I am using modern anachronistic location designations). This also narrows the timing of the trip to a departure between 5800 BCE and 5500 BCE, a mere 300 year window and probably closer to 5500 BCE than 5800 BCE. This leaves them in a wandering folk migration mode until they settle at Lake Chad, of at least 300 years and possibly 400-500 years, although one could imagine the trip being made a series of periodic spurts rather than continuously, settling down for a few generations here or there along the way, then uprooting themselves and moving on again, perhaps driven by climate change to continually uproot themselves until they reach their promised land.

    5. Im interested in the possibility that many cultures of pre-history scouted for not only islands, but distant lands that were favorable to their way of life and poorly defended. I'd give the example of the Polynesian scouting or post-exploration colonialism. So I'm definitely down with a possibility that pastoralist societies might send adventurers out to very distant lands to find favorable conditions for grazers and wagons. Obviously the wet phase Sahara had the right stuff for someone. It could be that instead of diffusion always, that some archaeological cultures literally packed up and headed VFR direct two thousand miles in one direction.

    6. Bug Dniester ? Steppe ?
      Seems far fetched
      You do realise that V88 was in El Trocs

    7. That's true, but Els Torcs was an epi-Cardial site which complicates it's relationship with the Bug-Dneister, Northern Nubia and the Levant.

      Bug-Dneister does have a wavy-line combed, point-based pottery tradition that has some ancient parallels in Nubia, and a theory by Dymtro Gaskevych below suggests contact or colonization between these remote places.

      Here's his abstract:
      "North-Pontic Impresso: Origin of the Neolithic Pottery with Comb Decoration in the South of Eastern Europe. Archaeologists so far have connected appearance of ware with pointed and rounded bottoms and comb decoration on the northern part of the Black Sea area with spread of inhabitants of northern and northeast regions to the south. Large series of absolute dates of Neolithic sites of Eastern Europe have been received in the Kiev radiocarbon laboratory recently. They have shown that such pottery appeared in the northern part of the Black Sea area earlier than on the Upper Dnieper region, the Volga river region, the Kama river basin and the Trans-Ural area. These data suggest incorrectness of existing hypotheses. Alternatively to these, the author proposes to regard North-Pontic Neo-lithic with comb decorated pottery as a part of the area of Mediterranean Neolithic cultures with Impresso ware. The possible Mediterranean prototype of the North-Pontic pottery with comb decoration could be ware of the North Africa Neolithic known as the «Saharan Sudanese Complex» or the «Khartoum Mesolithic». Formed in 9—8 thousand сal BC, in the middle 7 thousand сal BC it could diff use to the Near East, and further — to the Northern Black Sea coast. Radiocarbon dates show high speed of this process. It corresponds to concept of «leapfrog colonization» founded on a coasting (model of «maritime pioneers» by J. Zilhᾶo). Occurrence of the Neolithic pottery in the region only aft er formation of the Bosporus Strait which has united the Black Sea with the Mediterranean supports possible maritime colonization of the Northern coast of the Black Sea too. Sites left by the Mediterranean migrants with full «Neolithic package» have not been found in the northern part of the Black Sea area so far. It can result from their position on nowadays fl ooded fertile lowlands along the coast of the sea, the level of which rose more than 10 m over the last 8.5 thousand years. On the other hand, one fragment of the vessel with Cardium decoration was found on the Savran' site of the Bug-Dniester culture. It suggests settlement here of some Mediterranean makers of Cardium ware in the northern part of the Black Sea area, or of their contacts with local population. Availability of ware with comb and linear decoration, all attributes of which are met in ceramics of Impresso-ware zone, and also specifi c «Neolithic» fl int implements, bones of domestic animals, polished stone artifacts, found on Neolithic settlements of the North-Pontic area, also can be evidence of contacts of the local population with Mediterranean migrants who lived on the Black Sea coast.

      North-Pontic Impresso: Origin of the Neolithic Pottery with Comb Decoration in the South of Eastern Europe (In Russian) (PDF Download Available). Available from: https://www.researchgate.net/publication/314114394_North-Pontic_Impresso_Origin_of_the_Neolithic_Pottery_with_Comb_Decoration_in_the_South_of_Eastern_Europe_In_Russian [accessed Sep 28, 2017]."

      Possibly a scenario is a secondary expansion or reflux of Neolithized Hunger-Gatherers?

    8. Even if we accept the (rather isolated) arguement that the Impresso pottery originates in Nubia, it doesn't follow that a 'reflux' scenario is realistic. Hunter-forager -fishers specialise in the niches which they inhabit. They cannot just up and migrate from the Dniper riverine environments to Nubia & Lybia. Rather, any assimilated forager would be swept up *in the direction* of the Neolithic wave, not counter-coup.
      Secondly, given that we have Impresso/Cardial sites in Anatolia and Balkans, and attendant accompanying lineages such as Hg E-M78 as far as C-T culture in Ukraine itself, we have established chain of intermediary connections.
      Then there is the issue of a paucity of V88 in Ukraine Mesolithic, which is dominated by I2a2a1b. By contrast, V88 seems plentiful in Balkans, and probably the rest of southern Europe when further tested.
      Given that we now have established linked between Iberia and Africa during the Neolithic, is there a reason why the spread of V88 in Africa should not be linked to this ?

    9. I think central to that question is estimating just how far the Beaker phenomenon spread in Africa. There's a temptation always to shade part of a map as belonging to one culture or another, but there might have been Beaker islands pretty far out. It'd be interesting if they contributed significantly to modern Berbers, but not quite as open to Chaddic

    10. or rather, I should say V88 in the Chad basin

    11. Ok thanks both to you and Andrew for interesting hypotheses .
      To go OT slightly, would you be in a position to summarise what you thought the Oldalde study showed about BB as a whole ?

    12. The bifurcation of R-Y8447 seems to correspond to a solidly Middle Neolithic time frame, which would leave little time for a trek from Late Neolithic Eastern Europe to Africa IMHO. It also looks like the southern Middle East has both branches occur side by side, one extending into Europe, the other into Africa.

  2. "Given that we now have established linked between Iberia and Africa during the Neolithic, is there a reason why the spread of V88 in Africa should not be linked to this?"

    V88 is a sporadic minor clade in Iberia, and you'd expect a diaspora to extend in all directions at a time of a collapsing civilization. What was going on? The same large scale climate trends going on in the Sahara were also affecting the steppe making it more arid than it had been at any time in the last 3000 years by 5500 BCE.

    "At its largest, around 4000 BC, [Lake Chad] is estimated to have covered an area of 400,000 km², (approx. 154,000 sq miles). Lake sediments appear to indicate dry periods, when the lake nearly dried up, around 8500 BC, 5500 BC, 2000 BC, and 100 BC."

    Until about 5400 BCE, the B-D people were dependent heavily on local hunting and foraging which as Rob notes calls for local area knowledge, but by 5400 BCE after enduring a century of the worst drought in living or legendary memory, the B-D people in the D valley had adopted cattle herding and were able to produce a majority of their own food rather than being hunters in a drying out forest-steppe. Once they could leave, they did.

    V88 is the dominant Y-DNA type among men in the Sahel who speak Chadic languages, while it is rare or absent in the Berber populations situated between Lake Chad and Morocco. Most populations in Africa that are not Chadic where V88 is found are fairly near Chadic communities.

    Further, we know from archaeological data more or less exactly when and where the Chadic people came into being after a period when Lake Chad was abandoned due to climate and was just starting to be restored. The Chadic language speaking people have been cattle herders from their inception. And, it is much easier to herd cattle to Lake Chad via the Levant and the Nile than it is to do so via the straight of Gibraltar and what later on becomes an arid Sahara desert (although ca. 5200 BCE was a "green Sahara" period).

    Also, the likely source of V88 in Lake Chad, which is the forested steppe of the Dneiper River Valley is right on the Moldova-Ukraine border, so overlap with the Balkans and a make up that is somewhat atypical of Mesolithic Ukraine as a whole makes perfect sense, particularly given that one has to traverse the Balkans to get from the Dneiper River Valley to Africa.

  3. R1b in Baka and Bakola pygmies of Cameroon/Gabon:- https://www.researchgate.net/publication/24280655_Genetic_and_Demographic_Implications_of_the_Bantu_Expansion_Insights_from_Human_Paternal_Lineages

  4. R-V88 in Equatorial Guinea:
    "(..)Of these R1b1 samples, nine are defined by the V88 marker, which was recently discovered in Africa. As high microsatellite variance was found inside this haplogroup in Central-West Africa and a decrease in this variance was observed towards Northeast Africa, our findings do not support the previously hypothesised movement of Chadic-speaking people from the North across the Sahara as the explanation for these R1b1 lineages in Central-West Africa."

    1. "The present findings are also compatible with an origin of the V88-derived allele in the Central-West Africa, and its presence in North Africa may be better explained as the result of a migration from the south during the mid-Holocene."