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Thread: New DNA Papers - General Discussion Thread

  1. #2631
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    Quote Originally Posted by Darko View Post
    It's capsian not Caspian, capsian is a Neolithic culture in North Africa their name derived from the region of Gafsa in southern Tunisia.
    thanks

    https://www.youtube.com/watch?v=2wrDa0E7gbE


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna
    Son's mtDna = K1a4p

  2. #2632
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    H4a1-T152C!

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    Quote Originally Posted by vettor View Post
    https://www.gnxp.com/WordPress/2021/...he-bronze-age/

    https://pubmed.ncbi.nlm.nih.gov/33974848/

    Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula


    most likely already presented?

    Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen’s disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.
    Yes, in the ancient DNA section.
    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

  3. #2633
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    Insights into the Middle Eastern paternal genetic pool in Tunisia: high prevalence of T-M70 haplogroup in an Arab population

    I keep seeing a small frequency of F* in north africa but I can not tell if it is H as in(H2 previously haplogroup F3,[5] (P96, L279, L281, L284, L285, L286, M282)
    ) or G or somethign else although i think its mostly G. Does anyone have more information on what the F* in North Africa is?
    Maternal Uncle y-line= F0R1b1-L21

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  5. #2634
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    Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia

    https://www.nature.com/articles/s41598-021-94932-9


    https://www.nature.com/articles/s41598-021-94932-9.pdf


    Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age
    transformed the social and genetic structure of European societies. Present-day Croatia lies at the
    heart of ancient migration routes through Europe, yet our knowledge about social and genetic
    processes here remains sparse. To shed light on these questions, we report new whole-genome data
    for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia.
    In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity
    from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple
    closely related males suggesting a patrilocal social organisation. We also find in that community an
    unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the
    region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological
    evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual
    dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding
    an important data point to the substantial shift in ancestry that occurred in the region between the
    Bronze Age and today.


    8 x G2a ydna
    2 x I2a ydna
    1 x R1b
    1 X J
    1 x C
    Last edited by vettor; 08-18-2021 at 05:29 PM.


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna
    Son's mtDna = K1a4p

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  7. #2635
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    Probably some fuel for the Bell Beaker origin debate?

    At 2003 a mass grave of eight individuals was uncovered at Balatonkeresztúr-Réti dűlő site, belonging to ages between one and half to 45 years old found in a refuse pit. Mass graves are not rare at prehistoric sites, from the Neolithic to the end of the Copper Age (around 2500 BCE) it was, in fact, pretty common
    Preliminary results indicate an extremely exciting genetic makeup for the individuals of Kisapostag culture as it signalises recent immigration into the region. Their connection to the BBC can be demonstrated [Fig.4.], although it seems to be minor, and they rather represent a population previously unseen in Prehistoric Europe.

    https://agi.abtk.hu/images/5.abra.png


    https://agi.abtk.hu/images/4.abra.jpg

    https://agi.abtk.hu/en/news/news

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  9. #2636
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    Quote Originally Posted by vettor View Post
    Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia

    https://www.nature.com/articles/s41598-021-94932-9


    https://www.nature.com/articles/s41598-021-94932-9.pdf


    Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age
    transformed the social and genetic structure of European societies. Present-day Croatia lies at the
    heart of ancient migration routes through Europe, yet our knowledge about social and genetic
    processes here remains sparse. To shed light on these questions, we report new whole-genome data
    for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia.
    In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity
    from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple
    closely related males suggesting a patrilocal social organisation. We also find in that community an
    unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the
    region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological
    evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual
    dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding
    an important data point to the substantial shift in ancestry that occurred in the region between the
    Bronze Age and today.


    8 x G2a ydna
    2 x I2a ydna
    1 x R1b
    1 X J
    1 x C
    with over 2000 years of G2a2 in Dalmatia du eto these samples ...it shows a clear marker for Proto-Dalmatian and Dalmatian people ............in other words, they have been in modern Croatia for a long time


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna
    Son's mtDna = K1a4p

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  11. #2637
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    Quote Originally Posted by vettor View Post
    with over 2000 years of G2a2 in Dalmatia du eto these samples ...it shows a clear marker for Proto-Dalmatian and Dalmatian people ............in other words, they have been in modern Croatia for a long time
    Unfortunate that mtDNA H was not further defined.

  12. #2638
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    Quote Originally Posted by Saetro View Post
    Unfortunate that mtDNA H was not further defined.
    Are you in Chris R. site of alpine markers ? .............send him a private message....he comments here

    unsure of your markers ............but the trend for numbers above 13 ie, H13 and above seem to be anywhere from north-balkans to Scandinavia in the majority

    I have for my mtdna 50% of my matches in the eastern alps and 50% in sweden and gotland

    I am in your Y branch of T ...but i am negative for your sub-branch

    regards


    My Path = ( K-M9+, LT-P326+, T-M184+, L490+, M70+, PF5664+, L131+, L446+, CTS933+, CTS3767+, CTS8862+, Z19945+, BY143483+ )


    Grandfather via paternal grandmother = I1-CTS6397 yDna
    Great grandmother paternal side = T1a1e mtDna
    Son's mtDna = K1a4p

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  14. #2639
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    Quote Originally Posted by pmokeefe View Post
    Haplotype and Population Structure Inference using Neural Networks in Whole-Genome Sequencing Data
    Jonas Meisner, Anders Albrechtsen
    Abstract
    Accurate inference of population structure is important in many studies of population genetics. In this paper we present, HaploNet, a novel method for performing dimensionality reduction and clustering in genetic data. The method is based on local clustering of phased haplotypes using neural networks from whole-genome sequencing or genotype data. By utilizing a Gaussian mixture prior in a variational autoencoder framework, we are able to learn a low-dimensional latent space in which we cluster haplotypes along the genome in a highly scalable manner. We demonstrate that we can use haplotype clusters in the latent space to infer global population structure utilizing haplotype information by exploiting the generative properties of our framework. Based on fitted neural networks and its latent haplotype clusters, we can perform principal component analysis and estimate the ancestry proportions based on a maximum likelihood framework. Using sequencing data from closely related human populations, we demonstrate that our approach is better at distinguishing closely related populations than standard admixture and principal component analysis software. We further show that HaploNet is fast and highly scalable by applying it to genotype array data of the UK Biobank.
    what this haplgroup this samples

  15. #2640
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    Haplotype and Population Structure Inference using Neural Networks (UK results)

    Haplotype and Population Structure Inference using Neural Networks in Whole-Genome Sequencing Data
    Jonas Meisner, Anders Albrechtsen

    We also applied HaploNet to SNP array data of the UK Biobank dataset and infer population
    structure on a subset of 276732 unrelated with self-reported ethnicity as 'White-British' with a
    total of 567499 SNPs after quality control and  ltering. It took 9.6 hours to train HaploNet on
    the chromosome 2 with a window size of 128, a batch-size of 4096 for 30 epochs. The results
    are displayed for estimating ancestry proportions and inferring population structure using PCA
    in Figure 4 and S15, respectively. For K = 3, HaploNet infers three clear ancestral components
    that reflect English, Scottish and Welsh sources, where the English component has interestingly the
    strongest signal in the north/center of England, the Scottish component has the strongest signal in
    the Outer Hebrides and the Welsh component has the strongest signal in Southern Wales. For the
    population structure inferred using our PCA method, we capture similar structure in the top PCs,
    where we additionally see a component capturing the variation between North and South Wales.

    2020.12.28.424587v2.jpg
    Figure 4: Estimated ancestry proportions of the subset of unrelated self-identi ed 'White-British'
    individuals in the UK Biobank dataset using HaploNet for K = 3. Individuals are plotted by their
    birthplace coordinates and colored by their ancestry proportion for each of the three sources.
    YFull: YF14620 (Dante Labs 2018)

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