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Thread: Genetic Genealogy and Ancient DNA in the News

  1. #1491
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    Quote Originally Posted by rozenfeld View Post
    http://journals.plos.org/plosone/art...l.pone.0170940

    Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

    Henrik B. Hansen, Peter B. Damgaard, Ashot Margaryan, Jesper Stenderup, Niels Lynnerup, Eske Willerslev, Morten E. Allentoft

    PLOS

    Published: January 27, 2017
    http://dx.doi.org/10.1371/journal.pone.0170940

    Abstract

    Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA). In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad) applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements.
    I've performed D-stat co-analysis of early medieval Vikings (V) with recent relevant European populations

    qpDstat: parameter file: qpDstat.par
    ### THE INPUT PARAMETERS
    ##PARAMETER NAME: VALUE
    genotypename: merg3.geno
    snpname: merg3.snp
    indivname: merg3.ind
    popfilename: list_qpDstat
    allsnps: YES
    ## qpDstat version: 701
    number of quadruples 36
    0 Icelandic 12
    1 Norwegian 11
    2 English 10
    3 Polish 23
    4 Shetlandic 10
    5 Irish 24
    6 German 10
    7 Scottish 33
    8 Irish_Ulster 6
    9 French 61
    10 Dutch 275
    11 Swede 11
    12 Dane 172
    13 Viking 2
    14 Chimp 1
    jackknife block size: 0.050
    snps: 559109 indivs: 661
    number of blocks for jackknife: 548
    nrows, ncols: 661 559109
    result: Icelandic Dane Viking Chimp -0.0940 -3.722 123 149 2618
    result: Icelandic Swede Viking Chimp 0.0087 0.826 541 531 12790
    result: Norwegian Swede Viking Chimp 0.0181 1.837 545 525 12790
    result: English Swede Viking Chimp 0.0068 0.649 539 532 12790
    result: Polish Swede Viking Chimp 0.0051 0.519 534 529 12706
    result: Shetlandic Swede Viking Chimp 0.0029 0.265 534 531 12706
    result: Irish Swede Viking Chimp 0.0035 0.344 534 530 12706
    result: German Dane Viking Chimp -0.0997 -3.849 122 149 2606
    result: German Swede Viking Chimp 0.0038 0.360 536 532 12706
    result: Norwegian Dane Viking Chimp -0.0873 -3.508 123 147 2618
    result: Scottish Swede Viking Chimp 0.0061 0.633 539 532 12790
    result: Irish_Ulster Swede Viking Chimp 0.0096 0.900 538 528 12706
    result: Icelandic Norwegian Viking Chimp -0.0095 -1.426 530 540 12813
    result: French Swede Viking Chimp 0.0030 0.316 539 536 12790
    result: Dutch Dane Viking Chimp 0.0000 0.008 99 99 1306
    result: Dutch Swede Viking Chimp -0.0031 -0.286 100 101 1322
    result: Swede Dane Viking Chimp -0.1085 -4.122 121 151 2612
    result: Irish Dane Viking Chimp -0.0973 -4.072 122 148 2606
    result: Dane Swede Viking Chimp 0.1085 4.122 151 121 2612
    result: Polish Dane Viking Chimp -0.1159 -4.795 120 152 2606
    result: English Norwegian Viking Chimp -0.0114 -1.686 530 542 12813
    result: English Dane Viking Chimp -0.1059 -4.062 123 152 2618
    result: Polish Norwegian Viking Chimp -0.0125 -2.068 525 538 12728
    result: Shetlandic Norwegian Viking Chimp -0.0144 -2.031 523 538 12728
    result: Dane Norwegian Viking Chimp 0.0873 3.508 147 123 2618
    result: Irish_Ulster Dane Viking Chimp -0.1079 -4.114 122 151 2606
    result: Dutch Norwegian Viking Chimp -0.0254 -2.394 97 103 1322
    result: Shetlandic Dane Viking Chimp -0.1073 -4.206 122 152 2606
    result: Irish_Ulster Norwegian Viking Chimp -0.0076 -0.953 532 540 12728
    result: French Dane Viking Chimp -0.1043 -4.424 122 150 2618
    result: Irish Norwegian Viking Chimp -0.0139 -2.382 524 539 12728
    result: Scottish Dane Viking Chimp -0.0956 -4.072 123 149 2618
    result: German Norwegian Viking Chimp -0.0132 -1.952 527 541 12728
    result: Swede Norwegian Viking Chimp -0.0181 -1.837 525 545 12790
    result: Scottish Norwegian Viking Chimp -0.0123 -2.167 529 542 12813
    result: French Norwegian Viking Chimp -0.0152 -2.826 530 546 12813
    ## end of run
    Rplot001.png

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    Quote Originally Posted by paoloferrari View Post
    found in comment section from eurogenes:

    “Like Sugar in Milk”: Reconstructing the genetic history of the Parsi
    population

    http://biorxiv.org/content/biorxiv/e...28777.full.pdf
    Now it's officially published:

    https://genomebiology.biomedcentral....059-017-1244-9

    Open Access

    “Like sugar in milk”: reconstructing the genetic history of the Parsi population

    Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai†, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G. Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi, Kurush Dalal, Shagufta Khaliq, Syed Qasim Mehdi^, Lalji Singh, Mait Metspalu, Toomas Kivisild, Chris Tyler-Smith, Richard Villems† and Kumarasamy Thangaraj

    Genome Biology201718:110

    DOI: 10.1186/s13059-017-1244-9

    Received: 1 February 2017

    Accepted: 23 May 2017

    Published: 14 June 2017

    Abstract
    Background

    The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India.
    Results

    Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East.
    Conclusions

    Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest.

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    More ancient DNA from Hungary. Six of seven samples are males. Timespan is from the Late Neolithic (4900-4500 BC) to the Late Avar Period (8th-9th century AD)..

    A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis
    http://www.biotechniques.com/Biotech...es-366001.html

    Abstract: Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses. We assessed this method by comparing the aDNA results from one petrous bone processed using our novel method to its pair, which was processed using established protocols for sampling disarticulated petrous bones. We show a decrease in endogenous DNA and molecular copy numbers when the drilling method is used; however, we also show that this method produces more endogenous DNA and higher copy numbers than any postcranial bone. Our results demonstrate that this minimally-invasive method reduces the loss of genetic data associated with the use of other skeletal elements and enables the combined craniometric and genetic study of individuals with archeological, cultural, and evolutionary value.
    Paternal: R1b-U152+ L2+ ZZ48+ FGC10543+, Pietro della Rocca, b. 1559, Agira, Sicily, Italy
    Maternal: Haplogroup H4a1-T152C!, Maria Coto, b. ~1864, Asturias, Spain
    Mother's Paternal: Haplogroup J1+ FGC4745/FGC4766+ PF5019+, Gerardo Caprio, b. 1879, Caposele, Avellino, Campania, Italy
    Father's Maternal: Haplogroup T2b-C150T, Francisca Santa Cruz, b.1916, Garganchon, Burgos, Spain

    Avatar: Raetian bronze votive, Fritzens-Sanzeno Culture VI-V c. BC, Trentino-Alto Adige/Südtirol, Italy

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    Quote Originally Posted by R.Rocca View Post
    More ancient DNA from Hungary. Six of seven samples are males. Timespan is from the Late Neolithic (4900-4500 BC) to the Late Avar Period (8th-9th century AD)..

    A minimally-invasive method for sampling human petrous bones from the cranial base for ancient DNA analysis
    http://www.biotechniques.com/Biotech...es-366001.html

    Abstract: Ancient DNA (aDNA) research involves invasive and destructive sampling procedures that are often incompatible with anthropological, anatomical, and bioarcheological analyses requiring intact skeletal remains. The osseous labyrinth inside the petrous bone has been shown to yield higher amounts of endogenous DNA than any other skeletal element; however, accessing this labyrinth in cases of a complete or reconstructed skull involves causing major structural damage to the cranial vault or base. Here, we describe a novel cranial base drilling method (CBDM) for accessing the osseous labyrinth from the cranial base that prevents damaging the surrounding cranial features, making it highly complementary to morphological analyses. We assessed this method by comparing the aDNA results from one petrous bone processed using our novel method to its pair, which was processed using established protocols for sampling disarticulated petrous bones. We show a decrease in endogenous DNA and molecular copy numbers when the drilling method is used; however, we also show that this method produces more endogenous DNA and higher copy numbers than any postcranial bone. Our results demonstrate that this minimally-invasive method reduces the loss of genetic data associated with the use of other skeletal elements and enables the combined craniometric and genetic study of individuals with archeological, cultural, and evolutionary value.
    Perhaps, with the raw data someone could read also Y-DNA SNPs.

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    Paging through a new study only to find it has no y-dna but only mtDNA is like being served dinner and finding only a plate full of vegetables.
     


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    i am rather envious of this woman in the conference saying there is a super-interesting talk about ancient dna ....i try to stay tuned but as i said i do not have a twitter account :i hope someone more introduced in the field could gather more information from this conference than me

    https://twitter.com/Turi__King/statu...26028458184704

    http://isabs.hr/

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    Quote Originally Posted by paoloferrari View Post
    i am rather envious of this woman in the conference saying there is a super-interesting talk about ancient dna ....i try to stay tuned but as i said i do not have a twitter account :i hope someone more introduced in the field could gather more information from this conference than me

    https://twitter.com/Turi__King/statu...26028458184704

    http://isabs.hr/
    Nothing new. They're just repackaging the stuff we've seen in papers for a broader audience.

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    thank you very much!nothing new under this boiling sun as usual, better go to the seaside!

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    The Anzick genome proves Clovis is first, after all


    http://www.academia.edu/33464545/The...nedited_proof_



    "Abstract

    The close relatives who buried the Anzick infant ca. 12,800 cal BP made classic Clovis tools and were unequivocally the lineal genetic ancestors of all the living Native peoples of southern North America, Central America, and South America. Clovis-derived Fell I fishtail points track the rapid southward migration of this ancestral population all the way to Tierra del Fuego. Any hypothesized earlier populations, if they (improbably) ever existed, must have been replaced or genetically swamped by these Clovis descendants."

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