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Thread: Ancient DNA from Bronze Age Lebanon (Haber et al. 2017)

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    Ancient DNA from Bronze Age Lebanon (Haber et al. 2017)

    "The Canaanites inhabited the Levant region during the Bronze Age and established a culture which
    became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient
    Near Easterners of this period, left few surviving textual records and thus their origin and relationship
    to ancient and present-day populations remain unclear. In this study, we sequenced five wholegenomes
    from ~3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the
    Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day
    Lebanon to catalogue modern Levantine genetic diversity. We find that a Bronze Age Canaaniterelated
    ancestry was widespread in the region, shared among urban populations inhabiting the coast
    (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads.
    This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern
    migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay
    patterns, that admixture occurred 6,600-3,550 years ago, coinciding with massive population
    movements in the mid-Holocene triggered by aridification ~4,200 years ago. We show that presentday
    Lebanese derive most of their ancestry from a Canaanite-related population, which therefore
    implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find
    Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate this
    Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive
    conquests by distant populations such as the Persians and Macedonians.

    [...]

    The PCA shows that Sidon_BA clusters with three individuals from Early Bronze Age Jordan
    (Jordan_BA)
    found in a cave above the Neolithic site of ‘Ain Ghazal and probably associated with an
    Early Bronze Age village close to the site.13 This suggests that people from the highly differentiated
    urban culture on the Levant coast and inland people with different modes of subsistence were
    nevertheless genetically similar, supporting previous reports that the different cultural groups who
    inhabited the Levant during the Bronze Age, such as the Ammonites, Moabites, Israelites and
    Phoenicians, each achieved their own cultural identities but all shared a common genetic and ethnic
    root with Canaanites.
    15 Lazaridis et al.13 reported that Jordan_BA can be modelled as mixture of
    Neolithic Levant (Levant_N) and Chalcolithic Iran (Iran_ChL). We computed the statistic f4(Levant_N,
    Sidon_BA; Ancient Eurasian, Chimpanzee) and found populations from the Caucasus and Iran shared
    more alleles with Sidon_BA than with Neolithic Levant (Figure 2A). We then used qpAdm8
    (with parameter allsnps: YES) to test if Sidon_BA can be modelled as mixture of Levant_N and any other
    ancient population in the dataset and found good support for the model of Sidon_BA being a mixture
    of Levant_N (48.4± 4.2%) and Iran_ChL (51.6± 4.2%) (Figure 2B; Table S3).


    In addition, the two Sidon_BA males carried the Y-chromosome haplogroups39 J-P58 (J1a2b) and JM12
    (J2b)
    (Table 1 and S4; Figure S9), both common male lineages in the Near East today. We
    compiled frequencies of Y-chromosomal haplogroups in this geographical area and their changes over
    time in a dataset of ancient and modern Levantine populations (Figure S10), and note, similarly to
    Lazaridis et al.,13 that haplogroup J was absent in all Natufian and Neolithic Levant male individuals
    examined thus far, but emerged during the Bronze Age in Lebanon and Jordan along with ancestry
    related to Iran.
    All five Sidon_BA individuals had different mitochondrial DNA haplotypes40 (Table 1),
    belonging to paragroups common in present-day Lebanon and nearby regions (Table S5) but with
    additional derived variants not observed in our present-day Lebanese dataset.
    We next sought to estimate the time when the Iranian ancestry penetrated the Levant.

    Our results support genetic continuity since the Bronze Age and thus our large dataset of present-day Lebanese
    provided an opportunity to explore the admixture time using admixture-induced linkage
    disequilibrium (LD) decay.
    Using ALDER41 (with mindis: 0.005), we set the Lebanese as the admixed
    test population and Natufians, Levant_N, Sidon_BA, Iran_N, and Iran_ChL as reference populations.
    To account for the small number of individuals in the reference populations and the limited number
    of SNPs in the dataset, we took a lenient minimum Z-score=2 to be suggestive of admixture. The most
    significant result was for mixture of Levant_N and Iran_ChL (p=0.013) around 181 ± 54 generations
    ago, or ~5,000 ± 1,500 ya assuming a generation time of 28 years (Figure S11A ). This admixture time,
    based entirely on genetic data, fits the known ages of the samples based on archaeological data since
    it falls between the dates of Sidon_BA (3,650-3,750 ya) and Iran_ChL (6,500-5,500 ya). The admixture
    time also overlaps with the rise and fall of the Akkadian Empire which controlled the region from Iran
    to the Levant between ~4.4 and 4.2 kya. The Akkadian collapse is argued to have been the result of a
    widespread aridification event around 4,200 ya, possibly caused by a volcanic eruption.42; 43
    Archaeological evidence in this period documents large-scale influxes of refugees from Northern
    Mesopotamia towards the south, where cities and villages became overpopulated.44 Future sampling
    of ancient DNA from Northern Syria and Iraq may reveal if these migrants carried the Iran_ChL-related
    ancestry we observe in Bronze Age Sidon and Jordan.

    Although f4 tests showed that present-day Lebanese share significantly more alleles with Sidon_BA
    than other Near Eastern populations do, indicating genetic continuity, we failed to model the presentday
    Lebanese using streams of ancestry coming only from Levant_N and Iran_ChL (qpAdm rank1 p=
    8.36E-07), in contrast to our success with Sidon_BA.
    We therefore further explored our dataset by
    running ADMIXTURE45 in a supervised mode using Western hunter-gatherers (WHG), Eastern huntergatherers
    (EHG), Levant_N, and Iran_N as reference populations. These four populations have been
    previously13 found to contribute genetically to most West Eurasians. The ADMIXTURE results replicate
    the findings from qpAdm for Sidon_BA and show mixture of Levant_N and Iranian populations (Figure
    3A). However, the present-day Lebanese, in addition to their Levant_N and Iranian ancestry, have a
    component (11-22%) related to EHG and Steppe populations not found in Bronze Age populations
    (Figure 3A). We confirm the presence of this ancestry in the Lebanese by testing f4(Sidon_BA,
    Lebanese; Ancient Eurasian, Chimpanzee) and find that Eurasian hunter-gatherers and Steppe
    populations share more alleles with the Lebanese than with Sidon_BA (Figure 3B ). We next tested a
    model of the present-day Lebanese as a mixture of Sidon_BA and any other ancient Eurasian
    population using qpAdm. We found that the Lebanese can be best modelled as Sidon_BA 93±1.6% and
    a Steppe Bronze Age population 7±1.6% (Figure 3C; Table S6). To estimate the time when the Steppe
    ancestry penetrated the Levant we used, as above, LD-based inference and set the Lebanese as
    admixed test population with Natufians, Levant_N, Sidon_BA, Steppe_EMBA, and Steppe_MLBA as
    reference populations. We found support (p=0.00017) for a mixture between Sidon_BA and
    Steppe_EMBA which has occurred around 2,950±790 ya (Figure S11B ).
    It is important to note here
    that Bronze Age Steppe populations used in the model need not be the actual ancestral mixing
    populations, and the admixture could have involved a population which was itself admixed with a
    Steppe-like ancestry population. The time period of this mixture overlaps with the decline of the
    Egyptian empire and its domination over the Levant, leading some of the coastal cities to thrive,
    including Sidon and Tyre, which established at this time a successful maritime trade network
    throughout the Mediterranean. The decline in Egypt’s power was also followed by a succession of
    conquests of the region by distant populations such as the Assyrians, Persians, and Macedonians, any
    or all of whom could have carried the Steppe-like ancestry observed here in the Levant after the
    Bronze Age.

    In this report we have analysed the first ancient whole-genome sequence data from a Levantine
    civilization, and provided insights into how the Bronze Age Canaanites were related to other ancient
    populations and how they have contributed genetically to present-day ones (Figure 4).
    Many of our
    inferences rely on the limited number of ancient samples available, and we are only just beginning to
    reconstruct a genetic history of the Levant or the Near East as thorough as that of Europeans who, in
    comparison, have been extensively sampled. In the future, it will be important to examine samples
    from the Chalcolithic/Early Bronze Age Near East to understand the events leading to admixture
    between local populations and the eastern migrants. It will also be important to analyze samples from
    the Iron Age to trace back the Steppe-like ancestry we find today in present-day Levantines. Our
    current results show that such studies are feasible."


    Source: Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences

    Pretty much what I expected. I expect the J-P58 individual to carry YSC234 and suspect J2b here is J2b1.
    Last edited by Agamemnon; 05-26-2017 at 06:31 PM.
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    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
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    Looks like the PCA suffers from projection bias:

    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 Eurasian ancestry detected in Lebanese and lacking in BA Sidon might be the ANE.

    I doubt we can label this BA Sidon sample as Canaanite. It probably spoke early Semitic or proto-West Semitic but is too early for Iron-age Canaanite.

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    Quote Originally Posted by Callingstar View Post
    The Eurasian ancestry detected in Lebanese and lacking in BA Sidon might be the ANE.

    I doubt we can label this BA Sidon sample as Canaanite. It probably spoke early Semitic or proto-West Semitic but is too early for Iron-age Canaanite.
    I agree. Proto-Canaanite or broadly NW Semitic would be a better label for these samples. The increase in steppe admixture can be attributed to the incoming Mitannians during the MBA and to the later influx of Sea Peoples during the LBA collapse. Either way, these samples will probably plot right next to Samaritans, pretty neat. I think it's safe to conclude that the earliest NW Semitic speakers were by and large identical to Jordan_EBA. J1-P58 and J2b1 keep showing up, seems I was right about the latter having been more common in the region by the past.
    Last edited by Agamemnon; 05-26-2017 at 07:08 PM.
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    According to the supplemental data, the J1-P58 individual is J1-L818 (so YSC234-) while the J2b individual is J2b2-Z631 (so M205-), I spoke too fast

    I don't know much about J2b2, what I do know about J1-L818 though is that it has a prominent Jewish sub-branch (L816), otherwise this branch of P58 is quite rare.
    Last edited by Agamemnon; 05-26-2017 at 07:41 PM.
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    the mtdna HV1b1 of J-M12 (J2b) Sidon_BA male is rare but it's present in Yemenite Jews and Assyrians.

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    Quote Originally Posted by Agamemnon View Post
    According to the supplemental data, the J1-P58 individual is J1-L818 (so YSC234-) while the J2b individual is J2b2-Z631 (so M205-), I spoke too fast

    I don't know much about J2b2, what I do know about J1-L818 is that it has a prominent Jewish sub-branch (L816), otherwise this branch of P58 is quite rare.
    The J2b individual isn't J2b2, he is ancestral at J2b2 and some downstream positions and is most probably J2b1-M205, so you were actually right. Also, the J1 individual is just P58, we'll have to wait raw data for downstream clades.

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  15. #8
    What modern people are the closest to that Canaanite?

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    Quote Originally Posted by Pribislav View Post
    The J2b individual isn't J2b2, he is ancestral at J2b2 and some downstream positions and is most probably J2b1-M205, so you were actually right. Also, the J1 individual is just P58, we'll have to wait raw data for downstream clades.
    Yeah, checked the table again, I misread. So I probably didn't speak too fast after all. Thanks for making me notice! And I admit J2b2 made very little sense in that context, I was literally scratching my head when I saw that.

    Quote Originally Posted by Kaldo View Post
    What modern people are the closest to that Canaanite?
    The Sidon_BA samples will probably end up plotting with Samaritans, and Lebanese Christians as well (not sure about the latter).
    Last edited by Agamemnon; 05-26-2017 at 09:38 PM.
    מכורותיך ומולדותיך מארץ הכנעני אביך האמורי ואמך חתית
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    ᾽Άλλο δέ τοι ἐρέω, σὺ δ᾽ ἐνὶ φρεσὶ βάλλεο σῇσιν:
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    Quote Originally Posted by Pribislav View Post
    The J2b individual isn't J2b2, he is ancestral at J2b2 and some downstream positions and is most probably J2b1-M205, so you were actually right. Also, the J1 individual is just P58, we'll have to wait raw data for downstream clades.
    Thanks for this. I was just going to say the same thing.

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