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Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

Schubert, Mikkel, Mashkour, Marjan, Gaunitz, Charleen, Fages, Antoine, Seguin-Orlando, Andaine, Sheikhi, Shiva, Alfarhan, Ahmed H., Alquraishi, Saleh A., Al-Rasheid, Khaled A.S., Chuang, Richard, Ermini, Luca, Gamba, Cristina, Weinstock, Jaco, Vedat, Onar, Orlando, Ludovic·2017·Journal of Archaeological Science
DOI 10.1016/j.jas.2016.12.005
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  • Molecular sexing of mammal species and identification of first-generation hybrids generally requires no more than 1,000-10,000 mapped reads.

    “For example, a minimal threshold of 10,000-30,000 SNPs is commonly used for assessing genetic relationships of human individuals at intra-continental scales 331,332 but molecular sexing of mammal species and identification of first-generation hybrids generally requires no more than 1,000-10,000 mapped reads 200 .”

    From Ancient DNA analysis (2021) · cites this paper as [200]

    The Methods validation section reports that Zonkey achieved maximal sensitivity and specificity for identifying equine F1 hybrids with approximately 10,000 equine reads, and the Introduction reports high specificity with as few as 1,000 mapped sequences. The Hybridization report describes molecular sex estimation but gives no 1,000–10,000-read threshold for it. The Conclusions discuss extending hybrid identification to other mammals as a possibility, not an established general requirement. (LLM, conf=0.87)

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Research works printed but not linked: 30

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Cited by

Sorted by citations

  • Ancient DNA analysis

    Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411

    Self-citation

Metadata

Authors
Schubert, M., Mashkour, M., Gaunitz, C., Fages, A., Seguin-Orlando, A., Sheikhi, S., Alfarhan, A. H., Alquraishi, S. A., Al-Rasheid, K. A. S., Chuang, R., Ermini, L., Gamba, C., Weinstock, J., Vedat, O., & Orlando, L.
Venue
Journal of Archaeological Science
Publisher
Elsevier BV
Published
2017-02
Volume
78
Pages
147-157
ISSN
0305-4403
DOI
10.1016/j.jas.2016.12.005
Cited by
69
References
2
Language
en
Licence
Funders
  • Danish Council for Independent Research Natural Sciences (4002-00152B)
  • Danish National Research Foundation (DNRF94)
  • Villum Fonden (miGENEPI)
  • International Research Group Program (IRG14-08)
  • Deanship of Scientific Research, King Saud University
  • “Chaires d'Attractivité 2014” IDEX, University of Toulouse
  • Marie-Curie Intra-European Fellowship program (FP7-IEF-302617, FP7-IEF-328024)
  • British Academy/Leverhulme (SG121966)
  • European Research Council (681605)

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