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Thread: Complete Genome of the Tyrolean Iceman

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    Senior Member Oslaf's Avatar
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    Complete Genome of the Tyrolean Iceman

    Post From:http://dienekes.blogspot.com/2012/02/complete-genome-of-tyrolean-iceman.html
    I'll update this post once I read the paper. I could not locate a source for the data after a quick scan of the paper, but:
    After genotyping, we merged both HapMap and 1,000 Genomes genotypes with the Popres/Iceman-merged dataset, resulting in a final analysis dataset containing 125,729 SNPs. PCA was then performed on all samples, excluding the five 1,000 Genomes samples, which were subsequently projected onto the PC space inferred from the rest of the dataset.
    UPDATE: The Iceman's genome can be found at the http://icemangenome.net site.

    UPDATE I (Y-chromosome):

    From the paper:
    We addressed this issue here by analysing the G2a4-defining L91 SNP in 7,797 chromosomes from 30 regions across Europe. Fig. 3d shows the spatial frequency distribution of G2a4 throughout Europe. The highest frequencies (25 and 9%) occur in southern Corsica and northern Sardinia, respectively, (Fig. 3e) while in mainland Europe the frequencies do not reach 1%.
    UPDATE II (Autosomal DNA):

    In terms of autosomal DNA, the Iceman clearly clusters with modern Sardinians, and also appears slightly more removed than them compared to continental Europeans. Interestingly, at least as far as the PC analyssi shows, Sardinians appear to be intermediate between the Iceman and SW Europeans, rather than Italians. Perhaps, this makes sense if the Paleo-Sardinian language is indeed related to languages of Iberia.

    I don't see a downloadable version of the Iceman's genome at the icemangenome.net site, but I've asked the corresponding author for a PLINK/EIGENSOFT version of it. I anticipate that, as I've predicted, this will appear to be largely "Mediterranean" according to Dodecad v3, or "Atlantic_Med" according to the newer K12b calculator. It appears that there has indeed been Sardinian continuity against a backdrop of European discontinuity.

    UPDATE III (Sardinians):

    The Iceman's genome also places the Sardinian genetic isolate into new light. Two explanations have been proposed for the fact that Sardinians appear genetically distinctive vis a vis continental Europeans:
    1. Sardinians have lost due to drift alleles that were present in continental Europe
    2. Continental Europeans have gained alleles that were not present in their Sardinian-like ancestors
    The Iceman's genome argues strongly in favor of the latter hypothesis: continental Europeans, or, at least North Italians c. 5,300 years ago were more Sardinian-like, and they have become less Sardinian-like up to the present, probably due to an influx of new populations, carrying new alleles. As more ancient DNA is recovered, we will slowly witness the transformation of gene pools over time.

    Nature Communications 3, Article number: 698 doi:10.1038/ncomms1701

    New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

    Andreas Keller et al.

    The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

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    Senior Member Oslaf's Avatar
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    A first look at the genome of the Tyrolean Iceman
    Thanks to the publication of the Tyrolean Iceman's (reconstructed on the left) genome sequence, by Keller et al. (2012), I have been able to include him in a joint analysis with 2,671 other individuals, previously assembled for the K7b and K12b calculators of the Dodecad Project.

    I have essentially repeated the unsupervised ADMIXTURE analysis from scratch, with two differences:
    • The dataset now includes Oetzi, and
    • The number of markers has been reduced to 44,435 by intersecting the 166,770 SNPs used in K7b/K12b with the SNPs available for Oetzi

    http://dienekes.blogspot.com/2012/03/first-look-at-genome-of-tyrolean-iceman.html

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