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

Mikkel Schubert, Marjan Mashkour, Charleen Gaunitz, Antoine Fages, Andaine Seguin-Orlando, Shiva Sheikhi, Ahmed H. Alfarhan, Saleh A. Alquraishi, Khaled A.S. Al-Rasheid, Richard Chuang, Luca Ermini, Cristina Gamba, Jaco Weinstock, Onar Vedat, Ludovic Orlando

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Horses, asses and zebras, can produce first-generation F1-hybrids, despite their striking karyotypic and phenotypic differences. Such F1-hybrids are mostly infertile, but often present characters of considerable interest to breeders. They were extremely valued in antiquity, and commonly represented in art and on coinage. However, hybrids appear relatively rarely in archaeological faunal assemblages, mostly because identification based on morphometric data alone is extremely difficult. Here, we developed a methodological framework that exploits high-throughput sequencing data retrieved from archaeological material to identify F1-equine hybrids. Our computational methodology is distributed in the open-source Zonkey pipeline, now part of PALEOMIX (https://github.com/MikkelSchubert/paleomix), together with full documentation and examples. Using both synthetic and real sequence datasets, from living and ancient F1-hybrids, we find that Zonkey shows high sensitivity and specificity, even with limited sequencing efforts. Zonkey is thus well suited to the identification of equine F1-hybrids in the archaeological record, even in cases where DNA preservation is limited. Zonkey can also help determine the sex of ancient animals, and allows species identification, which advantageously complements morphological data in cases where material is fragmentary and/or multiple candidate equine species coexisted in sympatry.

Original languageEnglish
Pages (from-to)147-157
Number of pages11
JournalJournal of Archaeological Science
Volume78
DOIs
Publication statusPublished - 2017 Feb 1

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first generation
antiquity
documentation
candidacy
animal
art
present
methodology
Assemblages
Archaeology
Sequencing
Computational
Documentation
Specificity
Horse
Coinage
Species Identification
Open Source
DNA Preservation
Methodology

All Science Journal Classification (ASJC) codes

  • Archaeology
  • Archaeology

Cite this

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. / Zonkey : A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. In: Journal of Archaeological Science. 2017 ; Vol. 78. pp. 147-157.
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Schubert, M, Mashkour, M, Gaunitz, C, Fages, A, Seguin-Orlando, A, Sheikhi, S, Alfarhan, AH, Alquraishi, SA, Al-Rasheid, KAS, Chuang, R, Ermini, L, Gamba, C, Weinstock, J, Vedat, O & Orlando, L 2017, 'Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages', Journal of Archaeological Science, vol. 78, pp. 147-157. https://doi.org/10.1016/j.jas.2016.12.005

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.

In: Journal of Archaeological Science, Vol. 78, 01.02.2017, p. 147-157.

Research output: Contribution to journalArticle

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T2 - A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages

AU - Schubert, Mikkel

AU - Mashkour, Marjan

AU - Gaunitz, Charleen

AU - Fages, Antoine

AU - Seguin-Orlando, Andaine

AU - Sheikhi, Shiva

AU - Alfarhan, Ahmed H.

AU - Alquraishi, Saleh A.

AU - Al-Rasheid, Khaled A.S.

AU - Chuang, Richard

AU - Ermini, Luca

AU - Gamba, Cristina

AU - Weinstock, Jaco

AU - Vedat, Onar

AU - Orlando, Ludovic

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