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Thread: Genomic History of Neolithic to Bronze Age Anatolia, N Levant, and S Caucasus 2020

  1. #21
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    Quote Originally Posted by Johnny ola View Post
    Τy.Useful post as always!!!

    So EBA Levant is the Proto-Semitic chronological period.I also think Iran C related admixture never reached in big amounts the very southern parts of the Levant..hence why modern Arabs are less west asian admixed and less anatolian N compared to Cannanite populations.It would be very interesting also to found out one day what it was the languange before Semitic in the Levant and especially during the Natufian culture.It would be afroasiatic or not?
    Why don't you look at it from different perspective?
    That Semitic is nothing other than an Afroasiatic refugee with Meso-Iranian admixture? Hmmm

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  3. #22
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    Quote Originally Posted by shadowhite View Post
    Wow! Another HV1b3! This is the sibling branch of HV1b2.
    Other Y-DNA:

    Maternal 6X Great Grandfather J1-ZS10441

    Target: SUPREEEEEME_scaled
    Distance: 1.9563% / 0.01956275
    33.6 Levant_Ashkelon_LBA
    18.4 Iberia_Northeast_Empuries2
    11.8 Baltic_LTU_Late_Antiquity_low_res
    10.0 IRN_Hajji_Firuz_BA
    9.0 Canary_Islands_Guanche
    8.4 FRA_IA
    7.6 ITA_Ardea_Latini_IA
    1.2 CHN_Chuanyun_Historic

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  5. #23
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    nvm my earlier post, I found the 1240k dataset, it is here
    https://edmond.mpdl.mpg.de/imeji/col...j1HseOUbd1OaEo
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  7. #24
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    Quote Originally Posted by shadowhite View Post
    Genomic History of Neolithic to Bronze Age Anatolia,
    Northern Levant, and Southern Caucasus

    https://www.sciencedirect.com/scienc...92867420305092

    direct link:Full Paper:
    12 MB
    A special gift for you on the occasion of Festival Al Fitr
    https://www.mediafire.com/file/az3sb...-main.pdf/file

    Supplemental Information:

    https://www.mediafire.com/file/3lzab...tolia.rar/file
    Thanks for this.

    I'm getting an error message with the rar file of the supplementary material. Are others opening without an issue?

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  9. #25
    One of the authors sent me this link for the paper
    https://authors.elsevier.com/a/1b8UfL7PXcJR4

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  11. #26
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    Quote Originally Posted by Andrewid View Post
    Thanks for this.

    I'm getting an error message with the rar file of the supplementary material. Are others opening without an issue?
    Free after registration
    https://www.sciencedirect.com/scienc...id=author#mmc1

    or:

    Quote Originally Posted by pmokeefe View Post
    Supplemental Information for Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus
    Does not appear to be behind a paywall

    Document S1. Tables S2, S6–S8, and S10

    Table S1
    Details of AMS Radiocarbon Dating on Selected 95 Individuals after Quality Filtering, Related to Figure 2

    Table S3
    List of Ancient Populations Published by Previous Studies which Are Used in Our Analyses, Related to STAR Methods Grouping of individuals and nomenclature; Dataset.


    Table S4
    Outgroup f3-Statistics, Related to Figure 6 Shared genetic drift between each of the Late Chalcolithic/Bronze Age (LC-LBA) groups of the present study and a panel of Test populations compared to the distal population Mbuti. Test populations consist of 300 ancient and modern worldwide populations. f3-statistics were estimated on autosomal portion of the Human Origins (HO) SNPs with a minimum total Nş SNP per test of 50,000. The highest 40 f3-statistics are presented per LC-LBA group.


    Table S5
    Genetic Differences between Neolithic-Early Chalcolithic (N-EC) Populations and the Late Chalcolithic-Late Bronze Age (LC-LBA) with Respect to a Test Population Measured by f4(Mbuti,Test;Barcın_N/Büyükkaya_EC/TellKurdu_EC, LC-LBA), Related to Figure 6 Test populations include European and West Asians ancient populations. f4-statistics were estimated on the on the autosomal portion of the 1240K SNP panel and standard errors were estimated by 5 cM block jack-knifing. Significant values (|z-score| ≥ 3) indicate that Test shares more alleles with the LC-LBA than N-EC (positive sign) or vice versa (negative sign) and are annotated in bold. Results important for our interpretations are annotated in Italics.


    Table S9
    Assignment of Y Chromosome and Mitochondrial Haplogroups, Related to STAR Methods Sex determination and uniparental haplotypes.
    Last edited by shadowhite; 05-29-2020 at 08:55 AM.

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  13. #27
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    he second post was updated

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  15. #28
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    "The site of Arslantepe provides another representative example. At the beginning of EBA, archaeological evidence at the site strongly suggests the presence of a disruptive socio-political conflict that led to the occupation of Arslantepe by pastoral populations with a connection to the Caucasus. In PCA and f4-statistics, two individuals dating to this period show excess affinity with populations from the Caucasus and the Pontic steppe compared to their peers, while later Arslantepe_EBA individuals do not share this Caucasian affinity (Table S10). This implies that the postulated demic interaction must have been transient and of small scale, although the small sample size from Arslantepe_EBA (n = 4) may not be sufficient to detect it. Subtle gene flow is consistent with recent findings from the site, suggesting that the EBA pastoralists occupying the site were more likely well-established local groups moving around the mountains rather than intrusive groups from the Caucasus (Frangipane, 2014)."

    "A few notable exceptions provide rather anecdotal but nonetheless important evidence for long distance mobility and extended Y-haplogroup diversity.
    For example, individual ART038 carries Y-haplotype R1b-V1636 (R1b1a2), which is a rare clade related to other early R1b-lineages, such as R1b-V88 that was found in low frequency in Neolithic Europe (e.g., Haak et al., 2015) and R1b-Z2103—the main Y-lineage that is associated with the spread of “steppe ancestry” across West Eurasia during the early Bronze Age. However, R1b-V1636 and R1b-Z2103 lineages split long before (∼17 kya) and therefore there is no direct evidence for an early incursion from the Pontic steppe during the main era of Arslantepe. Lineage L2-L595 found in ALA084 (Alalakh) has previously been reported in one individual from Chalcolithic Northern Iran (Narasimhan et al., 2019) and in three males from the Late Maykop phase in the North Caucasus (Wang et al., 2019). These three share ancestry from the common Anatolian/Iranian ancestry cline described here, which indicates a widespread distribution that also reached the southern margins of the steppe zone north of the Caucasus mountain range."

    I can hear the champagnes popping open over at Carlos' place.
    Last edited by Dorkymon; 05-29-2020 at 10:19 AM.
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  17. #29
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    Quote Originally Posted by Dorkymon View Post
    "The site of Arslantepe provides another representative example. At the beginning of EBA, archaeological evidence at the site strongly suggests the presence of a disruptive socio-political conflict that led to the occupation of Arslantepe by pastoral populations with a connection to the Caucasus. In PCA and f4-statistics, two individuals dating to this period show excess affinity with populations from the Caucasus and the Pontic steppe compared to their peers, while later Arslantepe_EBA individuals do not share this Caucasian affinity (Table S10). This implies that the postulated demic interaction must have been transient and of small scale, although the small sample size from Arslantepe_EBA (n = 4) may not be sufficient to detect it. Subtle gene flow is consistent with recent findings from the site, suggesting that the EBA pastoralists occupying the site were more likely well-established local groups moving around the mountains rather than intrusive groups from the Caucasus (Frangipane, 2014)."

    "A few notable exceptions provide rather anecdotal but nonetheless important evidence for long distance mobility and extended Y-haplogroup diversity.
    For example, individual ART038 carries Y-haplotype R1b-V1636 (R1b1a2), which is a rare clade related to other early R1b-lineages, such as R1b-V88 that was found in low frequency in Neolithic Europe (e.g., Haak et al., 2015) and R1b-Z2103—the main Y-lineage that is associated with the spread of “steppe ancestry” across West Eurasia during the early Bronze Age. However, R1b-V1636 and R1b-Z2103 lineages split long before (∼17 kya) and therefore there is no direct evidence for an early incursion from the Pontic steppe during the main era of Arslantepe. Lineage L2-L595 found in ALA084 (Alalakh) has previously been reported in one individual from Chalcolithic Northern Iran (Narasimhan et al., 2019) and in three males from the Late Maykop phase in the North Caucasus (Wang et al., 2019). These three share ancestry from the common Anatolian/Iranian ancestry cline described here, which indicates a widespread distribution that also reached the southern margins of the steppe zone north of the Caucasus mountain range."

    I can hear the champagnes popping open over at Carlos' place.

    It's interesting to note that the R1b-V1636 sample was identified as a sacrificial victim at the Arslantepe palace, indicating that he might have belonged to an enemy population (presumably from the Armenian highlands), which as it looks like now was eventually ousted or defeated.

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  19. #30
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    Quote Originally Posted by marcelkolar View Post
    It's interesting to note that the R1b-V1636 sample was identified as a sacrificial victim at the Arslantepe palace, indicating that he might have belonged to an enemy population (presumably from the Armenian highlands), which as it looks like now was eventually ousted or defeated.
    Perhaps, but he still doesn't harbour any steppe ancestry on Vahaduo. He could have spoken an Indo-European language, but it becomes clearer with this paper that those people were acculturated, rather than being a mixed offspring of the Indo-Europeans. Perhaps with more samples this will change, but so far this is the picture that I'm seeing.

    Target: TUR_Arslantepe_LC:ART038
    Distance: 5.0900% / 0.05089989
    64.0 Anatolia_Barcin_N
    19.8 IRN_Ganj_Dareh_N
    9.8 GEO_CHG
    6.4 Levant_Natufian
    0.0 Baltic_LVA_HG
    0.0 IberomaurusianMAR_Taforalt
    0.0 Indian
    0.0 Nganassan
    0.0 RUS_Devils_Gate_Cave_N
    0.0 West_African
    0.0 WHG
    0.0 Yamnaya_UKR
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