May 17, 2013

Ancient Minoan mtDNA

Early Minoan jar
(CC by Wolfgang Sauber)
An ancient Minoan cave ossuary from Ayios Charalambos, Lasithi Plateau (around Mt. Ditke, Eastern Crete), dated to c. 2400-1700 BCE, has produced 37 valid mtDNA sequences (HVS-I).

Jeffrey R. Hughey et al., A European population in Minoan Bronze Age Crete. Nature Communications 2013. Open accessLINK [doi:10.1038/ncomms2871]

Abstract

The first advanced Bronze Age civilization of Europe was established by the Minoans about 5,000 years before present. Since Sir Arthur Evans exposed the Minoan civic centre of Knossos, archaeologists have speculated on the origin of the founders of the civilization. Evans proposed a North African origin; Cycladic, Balkan, Anatolian and Middle Eastern origins have also been proposed. Here we address the question of the origin of the Minoans by analysing mitochondrial DNA from Minoan osseous remains from a cave ossuary in the Lassithi plateau of Crete dated 4,400–3,700 years before present. Shared haplotypes, principal component and pairwise distance analyses refute the Evans North African hypothesis. Minoans show the strongest relationships with Neolithic and modern European populations and with the modern inhabitants of the Lassithi plateau. Our data are compatible with the hypothesis of an autochthonous development of the Minoan civilization by the descendants of the Neolithic settlers of the island.

From the paper (emphasis mine):

The majority of Minoans were classified in haplogroups H (43.2%), T (18.9%), K (16.2%) and I (8.1%). Haplogroups U5A, W, J2, U, X and J were each identified in a single individual

Figure 2: Minoan mtDNA haplotypes in extant and ancient populations.
(a) Minoan mtDNA HVS-1 haplotypes shared with the modern or ancient populations. (b) Frequency distribution of the 15 shared Minoan haplotypes among the various modern and ancient population groups.

I find very interesting that of the six non-singleton shared HVS-I sequences, four match those of Central European Neolithic (ht 5, 11, 13 and 14, plus singleton ht 4). The total percentage of coincidences is smaller than with Southern Neolithic but this grouping only has two matches with Minoan common haplotypes (ht 11 and 14, plus singleton ht 4), not any striking match.

Among modern populations the best fits seem to be the Balcans, Turkey and Middle East, both with five non-singleton matches out of six possible ones (ht 20 is only found in Turkey, click to expand if you don't see it, while ht 8 is found in the Balcans and the Middle East). 

So I would conclude that the Minoan sample fits well with a mix of Anatolian and Balcanic (or less likely Near Eastern) origin, after due founder effect, fitting also reasonably well with Danubian Neolithic and therefore with their likely (partial?) origins at the Balcanic Painted Ware Neolithic.

The greater pseudo-affinity with other populations, based only on overall frequency, seems to be inflated by four haplotypes only: ht 14 (the omnipresent CRS), ht 11 (apparently a common K variant), ht 4 (a relatively common T variant but only present in a single Minoan individual) and ht 12 (H5, again present only in an isolated case in the Minoan sample).

So let's please be careful and try not to mix quantity (frequency) with quality (relevant haplotype matches). 

The paper also includes a principal component analysis with a more detailed array of populations:


One of the most intriguing facts here is the near-identity between Minoan and modern Lasithi Plateau populations. It would seem logical but Wikipedia describes an instance of ethnic cleansing and later repopulation by the Venetians (emphasis mine):

The fertile soil of the plateau, due to alluvial run-off from melting snow, has attracted inhabitants since Neolithic times (6000 BC). Minoans and Dorians followed and the plateau has been continuously inhabited since then, except a period that started in 1293 and lasted for over two centuries during the Venetian occupation of Crete. During that time and due to frequent rebellions and strong resistance, villages were demolished, cultivation prohibited, and natives were forced to leave and forbidden to return under a penalty of death. A Venetian manuscript of the thirteenth century describes the troublesome plateau of Lasithi as spina nel cuore (di Venezia) - a thorn in the heart of Venice. Later, in the early 15th century, Venetian rulers allowed refugees from the Greek mainland (eastern Peloponnese) to settle in the plain and cultivate the land again.

Is this totally wrong? A brutal error? Erudite vandalism? I cannot say (and would appreciate knowledgeable feedback).

A clear issue is that the current inhabitants of the plateau have a distinctive genetic signature in their Y-DNA, quite different from that of other Cretans, with much higher frequencies of R1b and R1a and much much lower frequencies of the most common Cretan lineage: J2a1. However they also almost lack the main mainland Greek haplogroup E1b, what suggests that the recolonization from Peloponnese story is not correct either. 

Interestingly Cretan R1b, so important in Lasithi Plateau (almost 50%), is also largely derived from Western Europe (although the other half could be Balcanic), maybe via Italy, and cannot be ancestral to it (almost all the Western variant belongs to a derived subclade common in Italy, Central Europe and France: U152).

What is going on here then? I must admit that I do not really know.

Other very close populations in the PCA graph are Serbians (green star) and Bronze Age Sardinians (green rhombus). Take it as you wish. Bronze Age Sardinians are also top in the pairwise comparison table (the closest modern populations being Portuguese, Germans and Corsicans, also Neolithic Scandinavians). However these statistical analyses (both the PCA and the pairwise table) may well hide flaws (like the above mentioned confusion between quantity and quality), so I'd take them with the proverbial pinch of salt, as the confidence of the findings depends on the details of the methodology, not necessarily the best ones.

In any case, the general conclusions of the paper do not seem to be wrong: the Egyptian origin hypothesis is totally discarded and a Neolithic origin seems much more likely. However so many questions remain open...

16 comments:

  1. When it come ethnic cleansing by Venetians, such actions were often exaggerated even by those who committed them (Aztecs in the Mesoamerica for example have been shown to have claimed to have destroyed communities that actually persisted until the colonial times) and as is usual in these cases, female lineages probably fared better than male ones, providing continuity. Whatever was the case officially, it's very likely that unofficially the population persisted through the supposedly non-inhabited era - these kind of supposedly empty spots tend to disappear in closer scrutiny. Venetian sources claiming that the plateau was uninhabited from 1343 to 1514 should probably be seen as reflecting official Venetian stance more than reality - occupying powers often tend to make such claims, even today. But that should be relatively easy to prove or disprove by trying to find medieval remains from before the Venetian era or comparing the current makeup of the plateau's population to that of Peleponnese now.

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    1. Maybe you're right but I would really like to have this issue clear. Judging on the mtDNA PCA, there was never any population change of relevance since Minoan times, what makes sense considering it's an inner mountain district, surely less susceptible to any change.

      However judging on Y-DNA, there is a sharp contrast between Lasithi Plateau and the rest of the island, yet the lineages do not seem to fit with Mainland Greece either. The nearest data I have is for NE Peloponnese but it's more or less the same across mainland Greece, so it should be enough - particularly the oh-so-typical mainland Greek lineage E1b is almost totally absent in Lasithi Plateau.

      Lashiti Plateau has 42% R1b (unheard of anywhere else in Greece: less than 20% except in Chios, where it reaches 25%). We do not exactly what kind (in Heraklion about half of the R1b may be judged as Italian but it is just 7% of the overall pool, what would make the Italian input a reasonably low figure).

      I'm wondering if it might be (at leas largely) R1b-V88, often found among highland Sardinians as well. But no idea. It's very difficult to analyze.

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    2. If "villages were demolished, cultivation prohibited, and natives were forced to leave and forbidden to return under a penalty of death" is true would a combination of Venetian soldiers and Lashiti women fit the dna evidence?

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    3. "Venetian soldiers"

      http://en.wikipedia.org/wiki/Venice

      "but Venetian troops were still recruited from the lagoon, plus feudal levies from Dalmatia (the very famous Schiavoni or Oltremarini)[27] and Istria."

      and

      http://en.wikipedia.org/wiki/Stratioti

      "The stradioti were recruited in Albania, Greece, Dalmatia, Serbia and later Cyprus.[7][8][9][10] Most modern historians have indicated that the Stratioti were mostly Albanians"

      Just a thought.

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  2. Maju, there's no reason to take the high affinity between the Minoan and post-Neolithic Western European mtDNA with a pinch of salt. Instead what you should do is view it in the right context.

    This affinity is real, but mostly indirect. In other words, it's due to the same processes acting on the mainland European as well as Minoan mtDNA gene pools.

    That doesn't mean the Minoan mtDNA isn't in part closely related to early Neolithic mtDNA. Indeed, modern mainland European mtDNA also shows some links to early Neolithic mtDNA. However, what it does mean is that there was a shift in European mtDNA from the Neolithic to the Bronze Age that overall made it look very similar to the mtDNA of the Minoans. You obviously think this is a coincidence, but I can see from the data that it's not.

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    1. "... there's no reason to take the high affinity between the Minoan and post-Neolithic Western European mtDNA with a pinch of salt".

      There is and I explained it in the article: the statistical affinity seems product in part of greater frequency shared lineages but these are less shared lineages in fact. Before I try to look at any explanation, I try to understand the data, and the data to my critical eyes says that the affinity haplotype by haplotype is much greater with the NE Mediterranean than with Western Europe, which seems to be at least to some extent an statistical artifact.

      First look at the data haplotype by haplotype, please, and then we can discuss context, reasons, processes and whatever else, things that I do not have clear at all for this particular case.

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    2. In case you don't have it clear, the Minoan sample's non-singleton haplotypes match with modern population as follows:

      1. Balcans, Turkey and Middle East: 5/6
      2. Western, Southern Europe, etc: 4/6
      3. North Africa: 3/6

      The most parsimonious solution to the question of Minoan origins is therefore: Balcans + Anatolia (6/6 matches) at least judging on this sample. This solution is impossible not including Anatolia, the only region to have ht20. The Balcans could be replaced in the solution only by Middle East (both regions and only them have ht 8) but the Balcans share more percentage overall and are closer geographically.

      This is what I'm seeing. Regardless of context and possible prehistorical explanations, what possible flaw can you see in this reasoning, which I deem most parsimonious?

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    3. I'm not saying that the Minoan mtDNA doesn't show a close relationship to early Central European Neolithic mtDNA. It does.

      But you can't deny that overall the post-Neolithic European mtDNA, including Minoan mtDNA, isn't a good fit for early Central European and Southern European Neolithic mtDNA.

      So what happened after the Neolithic on mainland Western Europe that overall made the mtDNA there look very much like the Minoan mtDNA? And is it a coincidence that the Copper Age in Europe is now being exposed as a period of unusually high mobility?

      You can't ignore these questions based on the fact that the Minoan mtDNA shows more haplotype matches with early Central European Neolithic mtDNA than with post-Neolithic Western European mtDNA. Don't lose sight of the forest for the trees Maju.

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    4. "... you can't deny that overall the post-Neolithic European mtDNA (...) isn't a good fit for early Central European and Southern European Neolithic mtDNA".

      Actually I've been one of the first ones to highlight that. I won't deny that at all.

      There is one exception however: the Basque Country. Paternabidea looks totally modern to me (n=9): 56% H (incl. 22% H3), and the rest 11% of each U, K, HV and I (singletons). Today it is around 62% H, 18% U(xK) and around 6% for each of these: HV0, K and J. The changes are very minor and fit within the expected random fluctuations.

      Basque polyester bubble apart, the kind of changes we see are different: on one side we have the "Neolithic front wave" (LBK, Cardium), which seems to have suffered dramatic re-Europeanization (increase of H and to lesser extent U) after the first moments, and on the other we have some 'Paleolithic-continuity Neolithics' like those from Portugal with loads of H, much more than modern locals, which have suffered the opposite process, let's call it "Orientalization" or "Mediterranization", since those times.

      "You can't ignore these questions based on the fact that the Minoan mtDNA shows..."

      I may be "ignoring those questions" because I am first of all finding that Minoan aDNA belongs to its region (Eastern Mediterranean), so we must consider it within it and not compare apples and oranges and pretend on a mere statistical artifact that it has anything to do with Western or Central Europe. If it has something to do with other Neolithic phenomenons and particularly LBK, as you seem to reckon, it must be because both have partly the same Balcano-Anatolian origins.

      In principle here we are discussing ancient Minoan mtDNA. I'm open to your questions but I do not feel I am ignoring anything that should be considered re. Minoan aDNA.

      "So what happened after the Neolithic on mainland Western Europe that overall made the mtDNA there look very much like the Minoan mtDNA?"

      Nothing because what you say did not happen at all. It is a mere statistical artifact as I explained in the main entry: Western/Northern mtDNA pools have plenty of four haplotypes that are found among ancient Minoans, two of those are common (H-CRS and a common K variant) and the other two are singletons among Minoans. These four hts inflate the apportions but that is meaningless. We must look at haplotype diversity rather than frequency.

      In other words: I do not see any particular affinity between ancient Minoans and Western/Northern Europeans (sure: more than they have with North Africans but that was to be expected).

      "And is it a coincidence that the Copper Age in Europe is now being exposed as a period of unusually high mobility?"

      Not sure what you mean by "coincidence" here but I agree that in Central Europe (not the same as "Europe"!!!) there seems to be important demic changes in the Chalcolithic.

      Minoans were essentially a Bronze Age people, of the Balcanic-Anatolian Bronze, which begins some 1200 years before that of the rest of Europe (c. 3000 BCE vs c. 1800 BCE). IF there were more than anecdotal, isolated individual, migrations from the wider Aegean region into other parts of Europe at that time, we would expect them to bring the Bronze tech with them. They did not: therefore there was no meaningful migration from the SE to the rest of Europe in the Middle or Late Chalcolithic. It does not seem like there were any major migrations at the onset of Western Bronze either, although it's almost certain that increased trade and cultural contacts did happen then.

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  3. "The majority of Minoans were classified in haplogroups H (43.2%), T (18.9%), K (16.2%) and I (8.1%). Haplogroups U5A, W, J2, U, X and J were each identified in a single individual. "

    Kurds have these mtDNA haplogroups.

    Minoan mtDNA (N=37):
    H : 32.4% (12 samples, including one H5, one H7, one H13a1a)
    T : 18.9% (7 samples, including one T1, 3 T2, one T3, one T5)
    K : 16.2% (6 sample)
    HV : 8.1% (3 samples)
    I : 8.1% (3 sample, all I5a)
    U : 5.4% (2 samples, including one U5a)
    J : 2.7% (1 sample, J2)
    R0 : 2.7% (1 sample)
    W : 2.7% (1 sample)
    X : 2.7% (1 sample)


    Kurdish mtDNA (N=91):
    H: 20.9% (19 samples, including 2 H5, one H7, one H13a2, 2 H14, 3 H15)
    T: 5.5% (5 samples, including T1 and T2)
    K: 7.7% (7 samples)
    HV: 7.7% (7 samples)
    I: 3.3% (3 sample; including one I5a)
    U: 23.1% (21 samples, including 4 U1, 2 U2, 4 U3, one U4, 2 U5, 5 U7, 3 U8)
    J: 12.1% (11 samples, including 9 J1, 2 J2)
    R0: 2.2% (2 samples)
    W: 4.4% (4 samples)
    X: 1.1% (1 sample)

    http://kurdishdna.blogspot.com/2013/04/kurdish-mtdna-data-ix.html

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    1. There are notable differences in the apportions, but guess that should be expected.

      Whatever the case a Kurdish genetic blog sounds very interesting to me, and that is indeed a discovery! :D

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    2. I am from Crete and i strongly believe that Minoans have some kind of relation with ancient Kurdish populations.

      According to archaeologist Hubert La Marie the Minoan vocabulary has two types of language: one used a religious vocabulary close to Vedic Sanskrit, a kind of Proto-Vedic, the other was a ‘popular’ vocabulary akin to both Proto-Vedic and Proto-Iranian (the common root of Avestan and Old Persian) but with a few specific West-Iranian elements in both the grammar and vocabulary, close to Kurdish Gourani (the southern branch of Kurdish spoken in the Zagros mountains) and Dumili (a dying dialect spoken in the Anti-Taurus mountains near northern Cilicia).
      https://www.academia.edu/303303/Minoan_mantras._The_quiet_decipherment_of_Linear_A

      Today both Cilicia and Zagros mountains have Kurdish populations. Also there is a Minoan site in eastern Crete called Zakros (sounds like Zagros)
      https://en.wikipedia.org/wiki/Zakros

      Also living here in Crete I see that there are many similarities in human characteristics and morphology between people of eastern Crete and the Kurdish populations and the DNA analysis you mentioned above seems to prove it.

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  4. I can't agree the egyptian origin of cretians is discredited, but I do know the study is largely discredited because this geneticist went into areas he simply wasn't qualified. He claims he compares minoan dna to libyans, but basic science shows its not true, or if he did it, he did it in a poor and sloppy way. The Taureg of the Fezzan and Northern Chad in Libya have H haplogroup higher than any group in Europe or the world?

    How can you conclude the minoans are europeans but leave out the entire y-dna in a credible study? He did not compare the minoans to various groups in africa so his study is a joke given that is what evans thought they were. The only africans he included was modern egyptians, modern turko-arabic north africans who were not there in antiqity. It'd be like comparing modern new yorkers to native indians from mexico and concluding that north american indians are not related to mexican native indians.

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    1. The Tuareg have LOTS of H1 specifically, yes. It is a founder effect specific of them but has a North West African origin (H makes up >25% of NW African mtDNA lineages, notably H1, H3, H4 and H7, all of which seem to come from Iberia or France, probably in the LGM).

      → http://forwhattheywereweare.blogspot.com/2010/10/mitochondrial-dna-h1-in-north-africa.html
      → http://leherensuge.blogspot.com/2009/04/brief-review-of-recent-mtdna-h-info.html

      I can only say that NW African Berbers are not really representative of Egyptian genetics as such, but, on the other side characteristic Egyptian lineages like X1, M1, U6a or the various L(xM,N) ones are apparently not present in the Minoan sample, which only seems to have European or West Asian lineages and nothing looking African in any way.

      Archaeologically also Minoans appear to be original of either the local Neolithic or new flows from Anatolia (or both).

      Also modern Cretans at least, Y-DNA-wise appear less "African" than mainland Greeks, among whom the haplogroup E1b-V13 is very important (Cretans are instead dominated by J2, a West Asian lineage probably associated to Neolithic or post-Neolithic expansions in Europe and South Asia).

      → http://leherensuge.blogspot.com.es/2008/05/greek-y-dna-review-at-dienekes.html

      "How can you conclude the minoans are europeans but leave out the entire y-dna in a credible study?"

      It's not so easy to sequence ancient Y-DNA.

      "The only africans he included was modern egyptians"...

      Actually their high frequencies of H make them look Tuareg and not Egyptians.

      "... modern turko-arabic north africans who were not there in antiqity."

      That's an interpretation that I can't agree with. While Persians, Greeks, Arabs and Turks ruled Egypt, their genetic impact is surely negligible. After all Egypt was always very densely populated. Another thing is to reasonably imagine that in the Neolithic (and that's long ago) there were some flows from West Asia, especially into the Delta. I still think that much of the West Asian and even whatever European-like stuff that is in Egyptian genetics is derived from pre-Neolithic flows. Y-DNA J1 for example is a lineage that I find likely to have arrived to NE Africa (not just Egypt but also Sudan and the Horn) some time in the Upper Paleolithic, from where it must have expanded to NW Africa with Capsian culture (late UP, Epipaleolithic and even first Neolithic of this area).

      My opinion in any case.

      "It'd be like comparing modern new yorkers to native indians from mexico and concluding that north american indians are not related to mexican native indians."

      Not the same at all. We know that Egypt has been continuously populated at very high densities since at least dynastic times, probably earlier. And we do not know of any process of systematic colonization of the area, not even in the Arab-Islamic period, just lesser strategic settlements. Under the Ottomans Egypt was most of the time an autonomous state and they even fought on their own (allied with the Venetians but with only nominal Ottoman support), against the Portuguese for the routes to the Indies (they lost). Besides Cairo, which is an Arabic military foundation in the outskirts of Memphis, some occasional ancient Greek commercial outposts and the famous Mamluks (Circassian slaves that became the dominant elite for some time), there's no other relevant inflow of foreign peoples since Ancient Egypt that we know of. What you say is like claiming that Egyptians are half-Britons just because there was a British protectorate for about 150 years. Nope.

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  5. On this blog there is another group of refugees mentioned, who colonized tyrolia after fleeing the ottomans. There is no e1b in this group either.

    IE languages seem tied to r1b and r1a lineages. I doubt that greece is an exception. The E and J probably came in over time from non IE groups being assimilated.

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    1. Can you document your first claim? I never heard of such group ever before. Anyhow Tyrolia was inhabited since much earlier, I just hope you don't mean all Tyrolians?!

      As for the second claim: yawn! I have already stated many times why I disagree with such a fanatic irrational model.

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