The Minoans had a script that probably recounted a language rather than a proto-language in a somewhat phonetic way, but it has not been deciphered and the extant Minoan Linear A script appears to consist mostly of bureaucratic records of ration programs, taxes and religious sacrifices. My own impression is that Minoan bore a striking similarity to the non-Indo-European language of the Hattic people whose language was superceded by the Indo-European Hittites in the time period from ca. 2000 BCE to 1500 BCE, by which time Hattic had ceased to be used outside religious ceremonies.I found this interesting for two reasons. First off, I having only researched living languages in connection with my DNA articles thus far, I wasn't aware of this extinct, unclassified, potentially non-Indo-European language attested in Europe (on the island of Crete). Secondly, the idea that it "has not been deciphered" sounded intriguing.
While researching the subject, I came upon a linguistics doctoral thesis entitled The Structure of the Minoan Language by Gareth Owens of the National and Kapodistrian University of Athens, which proposes that the Minoan language was in fact an Indo-European language, and likely belongs to a separate branch of the language family than any of the living Indo-European languages. I found his reasoning to be quite convincing, as it is based not only on lexical similarities that could be explained by borrowing, but also on morphological similarities, including masculine, feminine and neuter noun declension patterns. Owens had studied the Minoan Language for approximately 15 years at the time this paper was written (2004), and stated:
It has now been possible to discuss and offer an interpretation, both etymologically and morphologically, for 50 words that constitute the Lexicon of the Minoan language. Linear A inscriptions, when read with Linear B sound values, and when interpreted in the Minoan cultural context, make sense as an Indo-European language of the Second Millennium B.C. . . I would place the Minoan language between Greek and Armenian as a distinct branch of the Indo-European family of languages, with whatever caveat we must keep in mind of what surprises scientific research may have for us in the future.With respect to the Y-DNA haplogroups of the Minoan speakers, according to an article entitled Middle Eastern and European mtDNA lineages characterize populations from eastern Crete by Laisel Martinez, Sheyla Mirabal, Javier R. Luis and Rene J. Herrera, published in the American Journal of Physical Anthropology, as quoted in Mathilda's Anthropology Blog:
Haplogroups J2a1h-M319 (8.8%) and J2a1b1-M92 (2.6%) [among the current population on Crete] were associated with the Minoan culture linked to a late Neolithic/Early Bronze Age migration to Crete ca. 3100 BCE from North-Western/Western Anatolia and Syro-Palestine (ancient Canaan, Levant, and pre-Akkadian Anatolia); Aegean prehistorians link the date 3100 BCE to the origins of the Minoan culture on Crete.Interestingly, y-DNA haplogroup J (common in the Caucasus, ancestral to both J2a1h and J2a1b1), along with haplogroup I (common where Germanic languages are spoken) are believed to correspond with the early Cro-Magnon settlement of Europe, while haplogroup R1a is commonly associated with the Indo-European expansion. Hopefully, further deciphering of the Minoan language inscriptions will shed light on the apparent divergence between the genetic and linguistic conclusions reached regarding the Minoan people.
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Update: According to a 2009 study by Underhill, 8.81% of the population of Crete are of haplogroup R1a1a. Perhaps ancient Minoans had a mixture of both J2 and R1a1a.
I no of no one who seriously argues for Y-DNA haplogroup J as a Cro-Magnon haplogroup (at least in Europe), although I is a very serious candidate (there is essentially no direct evidence on the question from ancient Y-DNA as it is not preserved as well as ancient mtDNA).
The evidence for Minoan not being Indo-European (which would be the most common view among linguists (see e.g. here and here, although you correctly note that not all agree on the poiint) includes some of the following:
1. The Minoan regime was ended quite dramatically by conquest at the hands of an Indo-European Mycenean society, and Minoan was not an evolutionary predecessor to Greek although Greek absorbed many pre-Greek loan words.
2. Egyptian phonetic transliteration of Minoan incantations doesn't sound like any Indo-European language while sounding similar to non-Indo-European languages of Western Anatolia.
3. The proper nouns of the Minoans bear a strong resemblance to non-Indo-European Anatolian and Aegean proper nouns.
4. There is no good evidence from contemporaneous and nearby Sumerian or Egyptian records of Indo-European peoples in Anatolia at the time it was settled from there. The Hittites are the first Indo-Europeans to enter written history in Anatolia, more than 1000 years after the Minoan civilization emerges. Minoans and likely fellow linguists were said to be linguistically very different from the earliest recorded Indo-Europeans (Mycenean Greeks and Hittites).
5. There are grammatical similarities between Minoan and other non-Indo-European languages like Etruscan. Eteocretian texts (Minoan language text in Greek writing) also suggest this. Notably, Minoan had no grammatic gender. There were also similarities in phonology.
6. Indo-European cultural "tells" like cremation and iconographic glorification of hte horse are absent among the Minoans, while Minoans have a bull cult that they lacked. In general, the archaeology cultures associated with Indo-Europeans don't reach Crete soon enough to be a fit.
R1a1a is likely of Mycenean provenance. The J2 is likely Anatolian (but Anatolia has had many successive languages over the years).
I'd also note that the cited author's identification of proto-Indo-European as dating to 7,000-8,000 BCE in the Aegean or Anatolia (the so called Anatolian view of proto-Indo-European) is quite at odds with the predominant view that Proto-Indo-European dates to the European Steppe of 3,500-4,500 BCE, of which Mallory is the most famous modern proponent.
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