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Thread: Genetic origins of Greeks by region (based on Y-DNA)

  1. #1

    Default Genetic origins of Greeks by region (based on Y-DNA)

    PCA graph with convex hulls (there are two main Y-DNA clusters) and loadings biplot:

    http://i.imgur.com/pbbyzjo.png



    Map of clustering and main haplogroups by region (based on data table and on PCA):

    https://i.imgur.com/lJx60C5.png



    Table with Y-DNA frequencies by region and two main haplogroups in each sample:

    https://i.imgur.com/jCg3PRx.png



    Now my question is, can you see any correlations with history of settlement, etc.?

    Basically, does it make any sense (especially these regional clusters of kinship)?

  2. #2
    conon394's Avatar hoi polloi
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    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Hard to comment without a source?

    Now my question is, can you see any correlations with history of settlement, etc.?
    You expect any? Especially when only looking a one gene. But how about sample size looks small and what the particular regions, how was the sample selected? Again without any insight into why/how the table was made its just a picture. Source is required.

    A bit sloppy - commas where it looks to need periods. Its unfortunate to have 3 different fonts for the numeral one and use capital i's, and some of the row do not add to one which could be slop or not but, I can't tell. In several cases there is a candidate with the same frequency as the selected second group why note one over the other?
    IN PATROCINIVM SVB Dromikaites

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  3. #3

    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    I think you need a higher resolution to get out of this what you want. The I in Greece has been there since the Mesolithic. The E, G, and J since the Neolithic expansion out of the Middle East, more may have arrived since. R1a and R1b are mostly associated with the Bronze Age expansion of Indo-European speakers.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  4. #4

    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Quote Originally Posted by conon394 View Post
    A bit sloppy - commas where it looks to need periods.
    Could be a result of a non-native speaker being the author. In some places, it is a comma and not a period, for example Germany.

  5. #5

    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Interesting new publication:

    "Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks":


    http://www.nature.com/ejhg/journal/v...hg201718a.html

  6. #6

    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    R1a is clearly Slavic, yet, assimilation... You can see that when you move towards south, rate of R1a reduces. "I" here, on the other hand, I tink it's "I2" like Balkan type of "I", not Scandinavian. "I2" is also Slavic and mostly found among Bosniaks and some other Balkan peoples.

    Northern Greeks (Thrace & Macedonia) (296 samples)
    I : 21.6
    R1a : 18.2
    R1b : 13.2
    E1b : 20.6
    G2 : 4.7
    J2 : 14.9
    J1 : 3.4
    LT : 2.7
    * : 0.7


    Central Greeks (Epirus & Thessaly) (127 samples)
    I : 12.6
    R1a : 11.8
    R1b : 10.2
    E1b : 31.5
    G2 : 6.3
    J2 : 18.1
    J1 : 3.9
    LT : 3.9
    * : 1.6


    Southern Greeks (Sterea Hellas & Peloponnese) (264 samples)
    I : 12.9
    R1a : 10.2
    R1b : 20.5
    E1b : 25.8
    G2 : 3.4
    J2 : 19.7
    J1 : 2.3
    LT : 3.8
    * : 1.5


    Eastern Greeks (Aegean islands & Ionia) (158 samples)
    I : 11.4
    R1a : 7.6
    R1b : 22.8
    E1b : 20.3
    G2 : 8.2
    J2 : 19.6
    J1 : 5.1
    LT : 3.2
    * : 1.9


    Cretan Greeks (Crete) (193 samples)
    I : 13.0
    R1a : 8.8
    R1b : 17.1
    E1b : 8.8
    G2 : 10.9
    J2 : 30.6
    J1 : 8.3
    LT : 2.6
    *: -


    All Greeks (1038 samples)
    I : 15.1
    R1a : 12.0
    R1b : 16.9
    E1b : 21.0
    G2 : 6.3
    J2 : 20.1
    J1 : 4.3
    LT : 3.2
    *: 1.1

    1.The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A
    Y Chromosome Perspective (Semino et.al) 2000
    2.Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns (Bosch et.al) 2005
    3.Y-chromosomal evidence of the cultural diffusion of agriculture in southeast Europe (Battaglia et.al) 2008
    4.Y-chromosomal evidence for a limited Greek contribution to the Pathan population of Pakistan (Firasat et.al) 2007
    5.Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects (Di Giaccomo et.al) 2003
    6.The coming of the Greeks to Provence and Corsica: Y-chromosome models of archaic Greek colonization of the western Mediterranean (King et.al) 2011
    7. Differential Y-chromosome Anatolian Influences on the Greek and Cretan Neolithic (King et.al) 2008
    A friend advises in his interest, not yours.

  7. #7
    neoptolemos's Avatar Breatannach Romanus
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    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Quote Originally Posted by Domen123 View Post
    Interesting new publication:

    "Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks":


    http://www.nature.com/ejhg/journal/v...hg201718a.html
    That's a great paper.
    Thanks for sharing.
    The similarities of Sicilians-Italians with the Pelopenesians was something to expected because it goes hand in hand with the various migrations back and forth from Greece to Italy vice versa during the millenia.
    Quem faz injúria vil e sem razăo,Com forças e poder em que está posto,Năo vence; que a vitória verdadeira É saber ter justiça nua e inteira-He who, solely to oppress,Employs or martial force, or power, achieves No victory; but a true victory Is gained,when justice triumphs and prevails.
    Luís de Camőes

  8. #8

    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Quote Originally Posted by River Lord View Post
    R1a is clearly Slavic, yet, assimilation... You can see that when you move towards south, rate of R1a reduces. "I" here, on the other hand, I tink it's "I2" like Balkan type of "I", not Scandinavian. "I2" is also Slavic and mostly found among Bosniaks and some other Balkan peoples.
    The general gist of what you're saying is almost certainly correct, but it's not really correct to refer to those haplotypes as Slavic and Slavs are almost certainly not the only ones who contributed them, even though the pattern you're observing may mostly be due primarily to Slavic migrations. Although I realize that you may have already known that and were using the terms as shorthand.

    To demonstrate what I mean, here is a list of all the ancient DNA finds of those two haplogroups from the Mesolithic to the Bronze Age:

    Spoiler Alert, click show to read: 
    I2a1 Mesolithic Sweden (Skoglund et al 2014)
    I2a1* Mesolithic Sweden (Haak et al 2015)
    I2a1a1a* Mesolithic Sweden (Haak et al 2015)
    I2a1a2a1a Mesolithic Lithuania (Mitnik et al 2017)
    I2a1b Mesolithic Sweden (Haak et al 2015)
    I2a1b Mesolithic Lithuania (Mitnik et al 2017)
    I2a1b Mesolithic Luxembourg (Lazaridis et al 2016)
    I2a1b* Mesolithic Sweden (Haak et al 2015)
    I2a2a Mesolithic Ukraine (Jones et al 2017)
    I2c2 Mesolithic Sweden (Haak et al 2015)

    I Neolithic Turkey (Mathieson et al 2015)
    I Neolithic Hungary (Szécsényi-Nagy et al 2015)
    I Neolithic Germany (Lazaridis et al 2016)
    I1 Neolithic Hungary (Szécsényi-Nagy et al 2015)
    I2a Neolithic Hungary (Gamba et al 2014)
    I2a Neolithic Hungary (Mathieson et al 2015)
    I2a1 Neolithic Croatia (Szécsényi-Nagy et al 2015)
    I2a1 Neolithic France (Lacan et al 2011) x5 indiviuals
    I2a1b1 Neolithic Spain (Lazaridis et al 2016)
    I2a1b1a Neolithic Germany (Haak et al 2015)
    I2a1b1a Neolithic Germany (Mathieson et al 2015)
    I2a2a1b2 Neolithic Spain (Lazaridis et al 2016)
    I2c Neolithic Turkey (Lazaridis et al 2016)

    I Bronze Age Italy (Allentoft et al 2015) x3 indiviuals
    I Bronze Age Spain (Mathieson et al 2015)
    I Bronze Age Hungary (Allentoft et al 2015)
    I Bronze Age Sweden (Allentoft et al 2015) x3 indiviuals
    I1 Bronze Age Sweden (Allentoft et al 2015)
    I2 Bronze Age Germany (Brandt et al 2013)
    I2a2b Bronze Age Germany (Schilz 2006) x4 individuals
    I2a2b Bronze Age Germany (Adler et al 2012)
    I2a2 Bronze Age Spain (Gómez-Sánchez et al 2014)
    I2a2 Bronze Age Spain (Mathieson et al 2015)
    I2a2a Bronze Age Hungary (Szécsényi-Nagy et al 2015)
    I2a2a Bronze Age Spain (Günther et al 2015)
    I2a2a1 Bronze Age Spain (Gómez-Sánchez et al 2014) x2 indiviuals
    I2a2a1 Bronze Age Hungary (Allentoft et al 2015)
    I2a2a1a2a Bronze Age Hungary (Allentoft et al 2015)
    I2a2a1b1b Bronze Age Russia (Allentoft et al 2015)
    I2c2 Bronze Age Germany (Adler et al 2012)

    R1a1* Mesolithic Russia (Lazaridis et al 2016)
    R1a1 Mesolithic Russia (Moussa et al 2016) x2 indiviuals
    R1a1 Mesolithic Russia (Chekunova et al 2014)
    R1a5 Mesolithic Estonia (Saag et al 2017)

    R1a Neolithic Ukraine (Jones et al 2017)
    R1a1 Neolithic Russia (Chekunova et al 2014) x2 indiviuals

    R1a Bronze Age Estonia (Saag et al 2017) x3 indiviuals
    R1a Bronze Age Germany (Adler et al 2012) x2 indiviuals
    R1a Bronze Age Germany (Mathieson et al 2015) x2 indiviuals
    R1a Bronze Age Russia (Allentoft et al 2015) x5 indiviuals
    R1a1 Bronze Age Latvia (Mitnik et al 2017)
    R1a1 Bronze Age Russia (Mathieson et al 2015) x2 indiviuals
    R1a1 Bronze Age Sweden (Allentoft et al 2015)
    R1a1 Bronze Age Germany (Brandt et al 2013) x3 indiviuals
    R1a1a Bronze Age Latvia (Mitnik et al 2017) x2 indiviuals
    R1a1a Bronze Age Germany (Mathieson et al 2015)
    R1a1a Bronze Age Russia (Keyser et al 2009) x2 indiviuals
    R1a1a Bronze Age Russia (Mathieson et al 2015)
    R1a1a1 Bronze Age Germany (Allentoft et al 2015)
    R1a1a1 Bronze Age Estonia (Mitnik et al 2017)
    R1a1a1 Bronze Age Denmark (Allentoft et al 2015)
    R1a1a1* Bronze Age Germany (Adler et al 2012
    R1b1a2 Bronze Age Denmark (Allentoft et al 2015)
    R1a1a1b Bronze Age Lithuania (Mitnik et al 2017) x3 indiviuals
    R1a1a1b Bronze Age Latvia (Mitnik et al 2017) x2 indiviuals
    R1a1a1b Bronze Age Russia (Mathieson et al 2015)
    R1a1a1b Bronze Age Russia (Allentoft et al 2015) x2 indiviuals
    R1a1a1b Bronze Age Sweden (Mitnik et al 2017)
    R1a1a1b1a2 Bronze Age Germany (Brandt et al 2013)
    R1a1a1b2 Bronze Age Mongolia (Hollard et al 2014) x4 indiviuals
    R1a1a1b2 Bronze Age Russia (Mathieson et al 2015) x4 indiviuals
    R1a1a1b2a Bronze Age Russia (Mathieson et al 2015)
    R1a1a1b2a2a Bronze Age Russia (Mathieson et al 2015)
    Quote Originally Posted by neoptolemos View Post
    That's a great paper.
    Thanks for sharing.
    The similarities of Sicilians-Italians with the Pelopenesians was something to expected because it goes hand in hand with the various migrations back and forth from Greece to Italy vice versa during the millenia.
    The things that are certainly correct in that paper, are things that were already known - specifically that there is a strong genetic affinity between Greeks and Italians (particularly southern Italians) and that the idea of complete medieval replacement is nonsense.

    From a scientific perspective though, that paper is pretty terrible. They don't cite or address the most important research on the topic and the one novel contribution they make was made by using publicly available software in a way it wasn't designed to be used and drawing conclusions based on their apparent misunderstanding about how the software works, which they don't check using formal statistics.

    Hellenethal et al 2014, using a methodology better for addressing the question, found that modern Greeks experienced an admixture event within the last one to two thousand years in which a population with Polish-like affinities contributed about 30% to the modern Greek genome. The rest of Greek affinities were more Mediterranean and to a lesser extent Near Eastern.

    The trouble with their ADMIXTURE runs is that they aren't using any outgroups and ADMIXTURE is only as accurate as what you feed into it. At each K level, you force admixture to further subdivide into populations, but only using Slavs and Greeks gives them all sorts of results that are wrong, wrong for reasons that would be obvious to anyone who knows about recent genetic research employing ancient samples. If they didn't know of the existence of the most important paper on their own topic though, that's probably too much to ask. Based on ancient DNA, we know that the majority of European ancestry can be attributed to four groups - Western Hunter Gatherers, Eastern Hunter Gatherers, Caucasus Hunter Gatherers, and Neolithic Levantine/Anatolian Farmers. The difference between Northern Europeans and Southern Europeans isn't a difference in ancestry so much as a difference in the proportions of those particular four groups. Running ADMIXTURE without outgroups causes the program to invent erroneous Northern European and Southern European ancestries because it can't identify the the structure correctly without seeing outgroups that don't have all four of those ancestries.
    Last edited by sumskilz; March 11, 2017 at 06:21 PM. Reason: formatting
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  9. #9
    Praeses
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    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Interesting stuff, still trying to get my head around all the lineages, but its less fuzzy now.

    Quote Originally Posted by sumskilz View Post
    ...- Western Hunter Gatherers, Eastern Hunter Gatherers, Caucasus Hunter Gatherers, and Neolithic Levantine/Anatolian Farmers...
    There's something very roleplaying about that list.

    Western Hunter Gatherers +1 STR, Spear and Thrown Spear proficiencies

    Eastern Hunter Gatherers +1 WIS, Herbal proficiency and start with bonus item from the healers list

    Caucasus Hunter Gatherers +1 DEX, Hunter's Charm Feat and self bow or axe proficiency

    Neolithic Levantine/Anatolian Farmers +1 END and start with 5kg grain
    Jatte lambastes Calico Rat

  10. #10

    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Quote Originally Posted by Cyclops View Post
    Interesting stuff, still trying to get my head around all the lineages, but its less fuzzy now.
    The reason those ancestries are clearly identifiable is that prior to the Holocene there was a lot less gene flow between groups, to the point that the people living on the two ends of what would become the fertile crescent were as genetically different from each other as Western Europeans are from East Asians today. People from the northern Fertile Crescent who were descended mostly from the Caucasus Hunter Gatherers expanded north of the Caucasus. Some of them came under the domination of Eastern Hunter Gatherers who had domesticated horses (for food at this point) and that was the ethnogenesis of Proto-Indo-Europeans. Eastern Hunter Gatherers lived from Central Asia to the Baltic, so they were only Eastern from a West Eurasian perspective, so your roleplaying stats might work better for these guys.

    Tying it back to the thread, the male Eastern Hunter Gatherer lineages were predominant in Proto-Indo-Europeans, so while they are also predominant in Slavs, some of them no doubt arrived in Greece with the language. Although they seem to have established themselves as a ruling class more than replace the Neolithic Farmers in Southern Europe.
    Quote Originally Posted by Enros View Post
    You don't seem to be familiar with how the burden of proof works in when discussing social justice. It's not like science where it lies on the one making the claim. If someone claims to be oppressed, they don't have to prove it.


  11. #11
    Praeses
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    Default Re: Genetic origins of Greeks by region (based on Y-DNA)

    Quote Originally Posted by sumskilz View Post
    The reason those ancestries are clearly identifiable is that prior to the Holocene there was a lot less gene flow between groups, to the point that the people living on the two ends of what would become the fertile crescent were as genetically different from each other as Western Europeans are from East Asians today. People from the northern Fertile Crescent who were descended mostly from the Caucasus Hunter Gatherers expanded north of the Caucasus. Some of them came under the domination of Eastern Hunter Gatherers who had domesticated horses (for food at this point) and that was the ethnogenesis of Proto-Indo-Europeans. Eastern Hunter Gatherers lived from Central Asia to the Baltic, so they were only Eastern from a West Eurasian perspective, so your roleplaying stats might work better for these guys.

    Tying it back to the thread, the male Eastern Hunter Gatherer lineages were predominant in Proto-Indo-Europeans, so while they are also predominant in Slavs, some of them no doubt arrived in Greece with the language. Although they seem to have established themselves as a ruling class more than replace the Neolithic Farmers in Southern Europe.
    There seems to be a lot of replacing from relatively small group of relatively large groups and I wonder about monoculture and genetic risk.

    I recently saw a documentary about the genetic diversity of three groups in Western South Africa/Namibia, the San, the Khoi and one other (I forget). Previously they were thought to be related genetically because of some shared languages (most are multilingual) but genetically they are completely distinct. The San turned out to have an amazing internal diversity, as well as pretty strong culture/language consistency as well as the highly distinctive DNA markers suggesting a largely "uncontaminated" descent.

    The scientist who did the genetic tests was clearly freaked out by the age of the Y-Chromosome lineages she had identified which she hinted at being over 200,000 years, but refused to say exactly on camera as she was obviously worried about some political consequences (that someone would misunderstand her as saying they were prehuman or something guess).

    If this is typical of premodern pockets of human population then the "Yamnaya bulldozer" effect may be one of a series of DNA simplifications in our genetic history. I know we will continue to see a steady turnover of mutation and other genetic drift to keep us diverse but a few generations of Genghis Khan types might see several pockets of diversity like the Khoi or San eliminated forever. If we simply our DNA enough...

    I guess globalisation will see a lot more interculture/"interracial" breeding and I think that tends to genetic health. I have to declare a position of mine here, my family is like the United nations with mostly British Isles but admixtures of Mauritian (boy are those people good looking, a complete genetic melting pot there), Japanese, East European Jew, Palestinian Muslim and other Middle Eastern, Japanese, Australian Aboriginal and others. We're a bit ashamed of the English bit, please don't hold it against me.

    Jk. But please.
    Jatte lambastes Calico Rat

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