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

Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages
Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages
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.
0305-4403
147-157
Schubert, Mikkel
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Mashkour, Marjan
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Gaunitz, Charleen
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Fages, Antoine
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Seguin-Orlando, Andaine
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Sheikhi, Shiva
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Alfarhan, Ahmed H.
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Alquraishi, Saleh A.
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Al-Rasheid, Khaled A.S.
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Chuang, Richard
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Ermini, Luca
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Gamba, Cristina
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Weinstock, Jacobo
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Vedat, Onar
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Orlando, Ludovic
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Schubert, Mikkel
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Mashkour, Marjan
fd19e11e-620b-4449-b68c-b3e438a89a89
Gaunitz, Charleen
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Fages, Antoine
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Seguin-Orlando, Andaine
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Sheikhi, Shiva
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Alfarhan, Ahmed H.
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Alquraishi, Saleh A.
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Al-Rasheid, Khaled A.S.
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Chuang, Richard
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Ermini, Luca
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Gamba, Cristina
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Weinstock, Jacobo
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Vedat, Onar
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Orlando, Ludovic
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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, Jacobo, Vedat, Onar and Orlando, Ludovic (2017) Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. Journal of Archaeological Science, 78, 147-157. (doi:10.1016/j.jas.2016.12.005).

Record type: Article

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.

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Accepted/In Press date: 15 December 2016
e-pub ahead of print date: 5 January 2017
Published date: 1 February 2017
Organisations: Archaeology

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Local EPrints ID: 405270
URI: http://eprints.soton.ac.uk/id/eprint/405270
ISSN: 0305-4403
PURE UUID: 224731db-b091-47da-9845-1870ff050fb3

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Date deposited: 02 Feb 2017 11:29
Last modified: 15 Mar 2024 06:16

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Contributors

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

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