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Thread: Ancient DNA Analysis of PPNB farmers

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    Ancient DNA Analysis of PPNB farmers

    Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

    Eva Fernández, Alejandro Pérez-Pérez, Cristina Gamba, Eva Prats, Pedro Cuesta, Josep Anfruns, Miquel Molist, Eduardo Arroyo-Pardo, Daniel Turbón



    The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B ( PPNB ) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700–6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.




    Some observations are very interesting:

    Two out of the 7 different complete PPNB haplotypes (16356C and 16293C, 28.57% of studied samples) were not represented in any of the modern and ancient populations of the database. From the remaining haplotypes only 16224C 16311C, the basal node of haplogroup K, was shared with the other two ancient populations, displaying a frequency of 9.52% in the Cardial/Epicardial dataset and of 23.08% in the LBK-AVK. This haplotype is distributed nowadays both in South Eastern Europe and the Near East with an average frequency of 4%. However, some populations such as Ashkenazi Jews, Csángó and Cyprus exhibit frequencies of this haplotype higher than 10% (Table S5, Figure 2).

    [...]

    Cluster 2 included our PPNB sample, grouped together with Ashkenazi Jews, Csángó, Cyprus and Cardial/Epicardial populations. High frequencies of haplogroups K and N* characterized this cluster (Table 2), pinpointing the genetic affinities between the PPNB and the Cardial/Epicardial Neolithic dataset already stressed by the qualitative haplogroup and haplotype analyses.

    [...]

    Cluster 2 was clearly distinguished from the other 5 clusters by PC4, which summed up a 6.64% of the global genetic variability (Table S8). The graphical plot of PC3 and PC4 separated populations by their frequencies of haplogroups HV, J and T (PC3) and K (PC4) (Figure S3). This graph situated the PPNB sample at the edge of PC4 axis, close to Cardial/Epicardial and Ashkenazi Jew populations.

    [...]

    Pairwise FST genetic distances were computed between the PPNB and the other populations of the database (Table S9). Non-significant pairwise FST values were obtained between PPNB and Cyprus (FST = 0.013; P = 0.2734), Ashkenazi Jews (FST = 0.028; P = 0.1087), Csángó (FST = 0.022; P = 0.1087) and Khoremian (FST = 0.0456; P = 0.0805). These populations also exhibited the lowest FST values. The highest significant distances corresponded to Gilaki, Caucasian Jews and Mazandarian populations (FST>0.2).

    [...]

    All the detected haplotypes but one -the basal node of haplogroup K- have a null or limited distribution in the modern genetic pool, suggesting that a great bulk of ancient Neolithic lineages were not integrated into their succeeding populations or were erased by subsequent population movements in the region. This is in agreement with previous observations from other Early Neolithic populations [27], [46], and underlines the importance of genetic drift processes at the beginning of the Neolithic [16]. Nevertheless, the multi-population comparative analyses performed here also suggest that certain population isolates of Middle Eastern origin, like the Druze, could have retained an ancient Neolithic genetic legacy through cultural isolation and endogamous practices [47]. Another interesting case are the Ashkenazi Jews, who display a frequency of haplogroup K similar to the PPNB sample together with low non-significant pairwise Fst values, which taken together suggests an ancient Near Eastern origin. This observation clearly contradicts the results of a recent study, where a detailed phylogeographical analysis of mtDNA lineages has suggested a predominantly European origin for the Ashkenazi communities [48]. According to that work the majority of the Ashkenazi mtDNA lineages can be assigned to three major founders within haplogroup K (31% of their total lineages): K1a1b1a, K1a9 and K2a2. The absence of characteristic mutations within the control region in the PPNB K-haplotypes allow discarding them as members of either sub-clades K1a1b1a or K2a2, both representing a 79% of total Ashkenazi K lineages. However, without a high-resolution typing of the mtDNA coding region it cannot be excluded that the PPNB K lineages belong to the third sub-cluster K1a9 (20% of Askhenazi K lineages). Moreover, in the light of the evidence presented here of a loss of lineages in the Near East since Neolithic times, the absence of Ashkenazi mtDNA founder clades in the Near East should not be taken as a definitive argument for its absence in the past. The genotyping of the complete mtDNA in ancient Near Eastern populations would be required to fully answer this question and it will undoubtedly add resolution to the patterns detected in modern populations in this and other studies.

    This is pretty much what I expected, I've been saying for years now that Cyprus might've retained much of the pre-Islamic Levant's Mediterranean-leaning genetic make up.
    Also, this study gives the lie to Costa et al's paper, unsurprisingly so.

    Needless to say, I am of the opinion that further aDNA studies (especially genome-wide studies of ancient samples) will add many more nails to the coffin of idiosyncratic theories proposing that modern-day Near Eastern populations have remained relatively untouched by admixture events and that Western Jews are "50% European hybrids".

    Any thoughts?
    Last edited by Agamemnon; 06-06-2014 at 06:08 PM.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
    יחזקאל פרק טז ג-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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    The low Fst to both Csángó and Khoremian poses further questions, such as what do ancient Near Easterners, a non-IE-speaking ethnic Hungarian group in Transylvania, and an Uzbek group have in common? Might this indicate a movement from Central Asia to the Near East? Or a radiating from the Near East to two different mountainous regions, where a motif has survived because of relative isolation?

    This is an interesting study but I would like to see this done with full mitochondrial sequencing, since premature conclusions have been drawn before based on HVR1-only analysis.
     

    Other ancestral Y lines:

    E1b-M81 Ukraine (Ashkenazi)
    E1b-V13 England
    I1-M253 Ireland
    I2-M423 Ukraine
    R1a-L176.1 Scotland
    R1b-L584 Syria/Turkey (Sephardi)
    R1b-L20 Ireland
    R1b-L21 (1)England; (2)Wales?>Connecticut
    R1b-L48 England
    R1b-P312 Scotland
    R1b-FGC32576 Ireland

    Other ancestral mtDNA lines:

    H1b2a Ukraine (Ashkenazi)
    H6a1a3 Ukraine
    K1a9 Belarus (Ashkenazi)
    K1c2 Ireland
    V7a Ukraine

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    This study revises the aDNA results which were first presented in a PhD thesis in 2005. At that stage they were pretty shaky, but I put them in my aDNA table as we had nothing else from that place and time. The more rigorous methodology now in use has resulted in the scrapping of several samples and the reallocation of others to altogether different haplogroups. It is quite a dramatic update (and it means that AJ needs yet more revision!) but I'm really pleased to have results that we can rely on. http://www.ancestraljourneys.org/was...ithicdna.shtml has been updated.

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    Quote Originally Posted by Agamemnon View Post
    ... Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands
    Eva Fernández, Alejandro Pérez-Pérez, Cristina Gamba, Eva Prats, Pedro Cuesta, Josep Anfruns, Miquel Molist, Eduardo Arroyo-Pardo, Daniel Turbón




    ...
    Doesn't this map and scenario have a min 1500 year discrepancy with Stuttgart EEF?

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    Quote Originally Posted by Agamemnon View Post
    Also, this study gives the lie to Costa et al's paper, unsurprisingly so. Needless to say, I am of the opinion that further aDNA studies (especially genome-wide studies of ancient samples) will add many more nails to the coffin of idiosyncratic theories proposing that modern-day Near Eastern populations have remained relatively untouched by admixture events and that Western Jews are "50% European hybrids". Any thoughts?
    I was very critical of the Costa et al. paper (another awful example of naive phylogeographic analysis). The odd thing was that most of the evidence that Costa et al. presented suggested a Near East origin for K, and yet they bizarrely concluded that a European origin was more likely.

    But doubts will remain until they publish the full sequence for these samples. I'm skeptical of ancient mtDNA haplogroup assignments that are based on just a few SNPs. They only report one CR SNP for one of their H samples. Hopefully they are working on full sequences.

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    Quote Originally Posted by GailT View Post
    I was very critical of the Costa et al. paper (another awful example of naive phylogeographic analysis). The odd thing was that most of the evidence that Costa et al. presented suggested a Near East origin for K, and yet they bizarrely concluded that a European origin was more likely.

    But doubts will remain until they publish the full sequence for these samples. I'm skeptical of ancient mtDNA haplogroup assignments that are based on just a few SNPs. They only report one CR SNP for one of their H samples. Hopefully they are working on full sequences.
    I completely agree with your assessment of the Costa et al paper, the conclusion seems dubious and rather contraditory to say the least.
    The conclusion that most AJ mtDNA lineages are of European extraction seems unconvincing as a whole and I'm pretty sure Behar will publish a rebuttal of the study.
    Seems this theory is about to experience a swift death...

    In fact, it's been several years that I, along with many others (such as Humanist, Baibars, ...) have been asking for genome-wide studies of ancient Near Eastern samples.
    This would be a great step towards a better understanding of Near Eastern genetic history, and would enlighten us further on the Neolithization of Europe.
    Until such a paper comes about, we can expect this topic to be highjacked by political activists of all kinds... Which troubles me more than anything else.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
    יחזקאל פרק טז ג-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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    Quote Originally Posted by Agamemnon View Post
    Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands

    Eva Fernández, Alejandro Pérez-Pérez, Cristina Gamba, Eva Prats, Pedro Cuesta, Josep Anfruns, Miquel Molist, Eduardo Arroyo-Pardo, Daniel Turbón

    Some observations are very interesting:

    This is pretty much what I expected, I've been saying for years now that Cyprus might've retained much of the pre-Islamic Levant's Mediterranean-leaning genetic make up.
    Also, this study gives the lie to Costa et al's paper, unsurprisingly so.

    Needless to say, I am of the opinion that further aDNA studies (especially genome-wide studies of ancient samples) will add many more nails to the coffin of idiosyncratic theories proposing that modern-day Near Eastern populations have remained relatively untouched by admixture events and that Western Jews are "50% European hybrids".

    Any thoughts?
    Also debunked by Lazaridis 2014...

    Present-day Near Eastern populations appear to have been strongly affected by events postdating movements of Neolithic migrants into Europe...
    Paternal: R1b-U152 >> L2 >> FGC10543 >> PR5365, Pietro Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: H4a1-T152C!, Maria Coto, b. ~1864, Galicia, Spain
    Mother's Paternal: J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain
    Paternal Great (x3) Grandfather: R1b-U106 >> L48 >> CTS2509, Filippo Ensabella, b.~1836, Agira, Sicily, Italy

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    Quote Originally Posted by Richard A. Rocca View Post
    Also debunked by Lazaridis 2014...
    And Haber et al 2013...

    We reconstructed the genetic structure of the Levantines and found that a pre-Islamic expansion Levant was more genetically similar to Europeans than to Middle Easterners.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
    יחזקאל פרק טז ג-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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    This is pretty much what I expected, I've been saying for years now that Cyprus might've retained much of the pre-Islamic Levant's Mediterranean-leaning genetic make up.
    Also, this study gives the lie to Costa et al's paper, unsurprisingly so.

    Needless to say, I am of the opinion that further aDNA studies (especially genome-wide studies of ancient samples) will add many more nails to the coffin of idiosyncratic theories proposing that modern-day Near Eastern populations have remained relatively untouched by admixture events and that Western Jews are "50% European hybrids".
    This is really interesting, any papers on the Y and mtDNA make up of Cyprus available?

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    Quote Originally Posted by Mehrdad View Post
    This is really interesting, any papers on the Y and mtDNA make up of Cyprus available?
    Unfortunately, the data about Cyprus is very scarce... Most of what we know about Cypriot uniparental lineages comes from Zalloua et al. 2008 ("Identifying Genetic Traces of Historical Expansions: Phoenician Footprints in the Mediterranean"), El Sibai et al. 2009 ("Geographical Structure of the Y-chromosomal Genetic Landscape of the Levant: A coastal-inland contrast") as well as Capelli et al. 2005 ("Population Structure in the Mediterranean Basin: A Y Chromosome Perspective").
    Cyprus is severely understudied, which is literally maddening given that it very likely retains much of the pre-islamic Levant's genetic make up (at least that's what the autosomal results are suggesting).

    I suspect Roy King also has access to unpublished data about Cyprus, which would prove very enlightening if you ask me.

    mnd made a thread about Cypriot Y-DNA frequencies not long ago, you might want to check it out.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
    יחזקאל פרק טז ג-


    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
    κρύβδην, μηδ᾽ ἀναφανδά, φίλην ἐς πατρίδα γαῖαν
    νῆα κατισχέμεναι: ἐπεὶ οὐκέτι πιστὰ γυναιξίν.


    -Αγαμέμνων; H Οδύσσεια, Ραψωδία λ

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